Diagnosing idh1 related subgroups and treatment of cancer

ABSTRACT

The invention relates to classification, diagnosis and treatment of cancers. In one embodiment, the present invention provides methods and kits that classify cancers into various subtypes based on expression patterns of AKT pathway components. In another embodiment, the present invention provides methods and kits that diagnose cancer subtypes by evaluating expression patterns of AKT pathway components. In still another embodiment, the present invention provides methods and kits that treat a cancer subtype by administering an alkylating agent or a PI3K/AKT/mTOR inhibitor to a patient. Cancers suitable with various embodiments of the invention include but are not limited to brain tumors, gliomas and GBM.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part of U.S. patent application Ser. No. 13/515,494, filed Jun. 12, 2012, currently pending, which is the national phase of International Patent Application No. PCT/US2010/059953, filed Dec. 10, 2010, which designated the U.S. and was published under PCT Article 21(2) in English. This application is a continuation-in-part of International Patent Application No. PCT/US2014/067168, filed Nov. 24, 2014, which designated the U.S. and was published under PCT Article 21(2) in English. This application also includes a claim of priority under 35 U.S.C. § 119(e) to U.S. provisional patent application No. 61/285,936, filed Dec. 11, 2009, now expired, and U.S. provisional patent application No. 61/907,987, filed Nov. 22, 2013, now expired. The contents of all the related applications cross-referenced herein are herein incorporated by reference in their entirety as though fully set forth.

STATEMENT REGARDING FEDERALLY-SPONSORED RESEARCH

This invention was made with government support under Grant No. NS064952-01A1 awarded by the National Institutes of Health. The government has certain rights in the invention.

FIELD OF THE INVENTION

The invention relates to medicine, for example, methods, compositions and kits for categorizing/classifying/stratifying and treating tumors.

BACKGROUND

All publications cited herein are incorporated by reference in their entirety to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference. The following description includes information that may be useful in understanding the present invention. It is not an admission that any of the information provided herein is prior art or relevant to the presently claimed invention, or that any publication specifically or implicitly referenced is prior art.

WHO grade IV astrocytoma or glioblastoma (GBM) are the most common primary brain tumors and, unfortunately, the most aggressive. Median survival of patients harboring these tumors is approximately 14 months. Despite a committed effort to investigate new chemotherapies, molecularly targeted therapies, immunotherapies, surgical and radiological approaches, there has been little improvement over the last 30 years. Inadequate classification of GBM may have contributed to the difficulty of developing new therapies by decreasing power of clinical trials and underestimating benefit of class-specific drugs. It may also have confounded discovery of class-specific pathways and drug targets.

GBM diagnosed by histopathology is a collection of molecular and clinical subtypes. For example, there are two classes of GBM based on clinical presentation [1], [2]. Primary GBM arise de novo in older patients and are associated with poorer prognosis. Secondary GBM are rare (˜5-10% of total GBM), progress from lower grade tumors, occur more frequently in younger patients with better prognosis and have a different molecular profile. Studies using gene expression, DNA copy number, miRNA, and DNA methylation show these molecular characteristics can divide GBM into subclasses, some with different clinical characteristics [3], [4], [5], [6], [7], [8], [9]. Three subtypes emerged in early studies of WHO grade IV GBM (studies that combine histological subtypes or grades of glioma and use molecular classification to distinguish them are excluded from this discussion). These were called proneural (PN), Proliferative (PROLIF) and mesenchymal (MES) and each had characteristic clinical and molecular features [4]. Later approaches find 3-5 GBM subtypes including the PN, MES and Classical (CLAS) subgroups [8], [9], [10], [11]. DNA methylation identifies a subset of PN tumors with glioma CpG island methylator phenotype (GCIMP) that are younger, longer surviving and tightly associated with IDH1 mutations [8].

However, molecular classification of GBM is still in its infancy. There is no consensus on the number of subtypes and which classifiers should be used to classify them. In addition, there is considerable reassignment of tumors to different classes depending on classifier used. There is also little information on which oncogenic pathways are active in subtypes and how subtypes respond to standard and experimental therapeutics.

Alterations in the growth factor receptor/phosphatidylinositol 3-kinase/AKT (GFR/PI3K/AKT) pathway occur in most human cancers including at least 85% of GBM [10]. Pharmacological inhibition of the GFR/PI3K/AKT pathway is a promising strategy for anti-cancer therapy [12], [13]. However, while sporadic responses have been reported, clinical trials of pathway inhibitors in GBM have been largely disappointing [14].

SUMMARY OF THE INVENTION

Various embodiments of the present invention provide a method for categorizing/classifying/stratifying a cancer in a subject. The method may consist of or may consist essentially of or may comprise: obtaining a biological sample from the subject; determining an expression pattern of AKT pathway components in the biological sample; and categorizing/classifying/stratifying the cancer based on the determined expression pattern of AKT pathway components in the biological sample.

Various embodiments of the present invention provide a method for diagnosing whether a subject has a cancer subtype. The method may consist of or may consist essentially of or may comprise: obtaining a biological sample from the subject; determining whether the cancer subtype's expression pattern of AKT pathway components is present in the biological sample; and diagnosing the subject as having the cancer subtype after the cancer subtype's expression pattern of AKT pathway components is determined to be present in the biological sample. In various further embodiments, the method comprises selecting, choosing or prescribing a therapeutic for the subject after diagnosis. In various further embodiments, the method comprises instructing or directing the subject to receive a therapeutic after diagnosis. In various further embodiments, the method comprises administering a therapeutically effective amount of a therapeutic to the subject, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of the diagnosed cancer subtype. In some embodiments, the cancer subtype is an AKT subtype including but not limited to C1, PN, MES, CLAS, SL, and PROLIF subtypes.

Various embodiments of the present invention provide a method for treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of a cancer subtype in a subject. The method may consist of or may consist essentially of or may comprise: obtaining a biological sample from the subject; determining whether the cancer subtype's expression pattern of AKT pathway components is present in the biological sample; providing a therapeutic; and administering a therapeutically effective amount of the therapeutic to the subject after the cancer subtype's expression pattern of AKT pathway components is determined to be present in the biological sample, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of the cancer subtype. In some embodiments, the cancer subtype is an AKT subtype including but not limited to C1, PN, MES, CLAS, SL, and PROLIF subtypes.

Various embodiments of the present invention provide a method for treating an AKT cancer subtype in a subject. The method may consist of or may consist essentially of or may comprise: providing a therapeutic; and administering a therapeutically effective amount of the therapeutic to the subject, thereby treating the AKT cancer subtype in the subject.

Various embodiments of the present invention provide a kit for categorizing/classifying/stratifying a cancer in a subject and/or for diagnosing whether a subject has a cancer subtype. The kit may consist of or may consist essentially of or may comprise: one or more detection agents that specifically bind to one or more AKT pathway components; instructions for using the one or more detection agents to classify the cancer in the subject, and/or diagnose whether a subject has the cancer subtype.

Various embodiments of the present invention provide a kit for treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of a cancer subtype in a subject. The kit may consist of or may consist essentially of or may comprise: one or more detection agents that specifically bind to one or more AKT pathway components; a quantity of a therapeutic; and instructions for using the one or more detection agents and the therapeutic to treat, prevent, reduce the likelihood of having, reduce the severity of and/or slow the progression of the cancer subtype in the subject.

Various embodiments of the present invention provide a kit for treating an AKT cancer subtype in a subject. The kit may consist of or may consist essentially of or may comprise: a quantity of a therapeutic; and instructions for using the therapeutic to treat the AKT cancer subtype in the subject.

Various methods, compositions, and kits of the present invention find utility in the classification and treatment of various tumors, including but not limited to various forms of brain tumors.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

Exemplary embodiments are illustrated in referenced figures. It is intended that the embodiments and figures disclosed herein are to be considered illustrative rather than restrictive.

FIGS. 1A-1D depict, in accordance with various embodiments of the invention, that AKT pathway gene expression classifies GBM. (FIG. 1A) Consensus heat maps for k=5 to 8 generated with AKT pathway genes in the discovery dataset (GBM195). Red indicates total consensus (consensus index of 1) while white indicates no consensus (consensus index of 0). (FIG. 1B) Silhouette scores for k=5 to 8 were calculated as described [26]. Samples with negative silhouette scores were removed in all further analysis. (FIG. 1C) Consensus CDF for k=2 to 10. (FIG. 1D) Effect of k on survival differences between subgroups. Kaplan Meier curves of patient subgroups were generated for k=2 to 10. For each k, Bonferroni corrected log rank p values were generated by pairwise comparison of subtypes. The smallest pairwise p value for each k is plotted.

FIGS. 2A-2D depict, in accordance with various embodiments of the invention, validation of AKT subgroups in an independent dataset. AKT pathway genes in discovery (FIG. 2A) and validation (FIG. 2B) datasets have similar patterns of expression in subgroups. Tumors in the discovery and validation set were first grouped by AKT subgroup membership then ordered by correlation coefficient. AKT gene order in the discovery set was determined by one-way hierarchical clustering and retained in the validation set. Discovery (FIG. 2C) and validation (FIG. 2D) datasets have similar DNA CNA. The percentage of patients in the discovery (FIG. 2A) and validation (FIG. 2B) datasets with copy number gains or losses in chr7, 10 and 19q is shown.

FIG. 3 depicts, in accordance with various embodiments of the invention, Akt classification for 5 glioblastoma subgroups. Previous classification systems distribute non-randomly in AKT subgroups. Distribution of Phillips (top), TCGA (middle) and G-CIMP (bottom) subgroups in AKT subgroups.

FIGS. 4A-4D depict, in accordance with various embodiments of the invention, that AKT subgroups are prognostic. Kaplan Meier survival curves plotted for Phillips (FIG. 4A) and AKT (FIG. 4B) subgroups in the discovery dataset and for TCGA (FIG. 4C) and AKT (FIG. 4D) subgroups in the validation dataset. Log rank p value=0.0005 (FIG. 4B; SL vs. rest); 0.0029 (B; PROLIF vs. rest) and 0.003 (FIG. 4D; SL vs rest). Survival differences did not reach significance in (FIG. 4A) and (FIG. 4C).

FIG. 5 depicts, in accordance with various embodiments of the invention, evidence that SL subtype (AKT subgroup 5) patients are sensitive to alkylating agents BCNU and CCNU. Kaplan Meier survival curves for TCGA patients receiving (solid line) or not receiving (dashed line) alkylating agent (BCNU and/or CCNU) by subgroup. p=0.03 after correcting for age (SL subtype; log rank). n=6 and 16 for SL patients receiving or not receiving BCNU/CCNU, respectively.

FIGS. 6A-6B depict, in accordance with various embodiments of the invention, that AKT subgroups have distinct genomic alterations. (FIG. 6A) Copy number alterations in TCGA AKT subgroups. The GISTIC method was applied to TCGA samples in each subgroup with copy number information. Data are presented as a G score which is an integrated score of the prevalence of the copy-number change times the average (log 2-transformed) amplitude. The green line shows significance threshold (FDR q values to account for multiple-hypothesis testing). Regions with subgroup-specific CNA are highlighted in yellow. (FIG. 6B) Distribution of clinical information and mutations, CNA and mRNA expression for glioma-associated genes in AKT subgroups. The 218 TCGA GBM cases with gene expression, consensus putative copy number alteration and validated mutation data [55], [56] was used for this analysis (The cBio Cancer Genomics Portal; http://www.cbioportal.org/). Gene expression is represented as z scores calculated relative to diploid tumors for each gene and are the median value of 3 mRNA platforms (Affymetrix U133A and Exon arrays and Agilent custom array). There was a statistically significant enrichment of IDH1 mutations in the SL and EGFR and CDKN2A mutations plus CNA in the CLAS subtype (p<0.02).

FIGS. 7A-7D depicts, in accordance with various embodiments of the invention, that subgroups have distinct patterns of expression for PI3K/AKT/mTOR pathway components (distinct Akt pathway activation). Tumors (x axis) were grouped by AKT class then Z transformed mRNA (FIG. 7A) or protein and phospho-protein expression (FIG. 7B) color coded to reflect magnitude (y axis). The Pearson correlation coefficient for AKT pS473 vs. RPS6 pS235/236 (light gray) and AKT pS473 vs. RPS6 pS240/244 (dark gray) for each subgroup is shown (FIG. 7C). Proposed AKT/mTOR/S6 pathway map for the MES and SL subtypes based on this data (FIG. 7D). This model shows loss of AKT and mTOR inhibitors (PHLPP, TSC and pAMPK) increases output of the AKT/mTOR/S6 axis (pRPS6) in the MES subgroup. Conversely, increased expression of these inhibitors decreases output in the SL subgroup. Red, grey and green represent high, intermediate and low expression/activity, respectively. Dashed line is indirect interaction.

FIGS. 8A-8B depicts, in accordance with various embodiments of the invention, summary of features in AKT subtypes (AKT C1/subgroup 1; AKT PN/subgroup 2; AKT MES/subgroup 3; AKT CLAS/subgroup 4; AKT SL/subgroup 5; AKT PROLIF/subgroup 6). Clinical and molecular features of AKT subgroups are summarized in (FIG. 8A). Illustration of proposed neurodevelopmental cell of origin for AKT subgroups based on GO terms (FIG. 8B). ND=not determined.

FIG. 9 depicts, in accordance with various embodiments of the invention, consensus k-means heat maps for k=2 to 10 generated with AKT pathway genes in the discovery dataset (GBM195). Red indicates total consensus (consensus index of 1) while white indicates no consensus (consensus index of 0).

FIG. 10 depicts, in accordance with various embodiments of the invention, average expression of AKT pathway genes in subgroups. Hierarchical clustering using AKT pathway genes was used to group GBM patients and genes in the discovery (GBM 195) dataset. Tumors in the validation dataset were grouped by AKT class keeping the same order of genes. The expression of AKT pathway genes in each class was averaged and is shown as a heatmap; red and green respectively represent high/increased and low/decreased average expression relative to the median of all tumors. Black represents minimal expression difference relative to the median of all tumors. The status of increased expression, decreased expression, or expression not changed significantly (minimal expression difference) of AKT pathway genes are also listed in Table 6.

FIG. 11 depicts, in accordance with various embodiments of the invention, Log 2 (tumor/normal) DNA copy number in subgroups. Amplifications (red) and deletions (blue) in subgroups (y axis) were determined by segmentation analysis of normalized signal intensities from TCGA SNP arrays using GISTIC and viewed with IGV by chromosomal location (x axis).

FIGS. 12A-12B depict, in accordance with various embodiments of the invention, distribution of clinical and molecular information by subgroup in the discovery dataset (GBM195). The table lists the number of tumors with the specified feature in each subgroup in the discovery dataset. Features with statistically significant enrichment in a subgroup after Bonferroni correction (p<0.05) are highlighted.

FIGS. 13A-13B depict, in accordance with various embodiments of the invention, distribution of clinical and molecular information by subgroup in the validation dataset (TCGA). The table lists the number of tumors with the specified feature in each subgroup in the validation dataset. Features with statistically significant enrichment in a subgroup after Bonferroni correction (p<0.05) are highlighted in dark grey. Features with statistically significant enrichment in a subgroup before Bonferroni correction are highlighted in light grey.

FIG. 14 depicts, in accordance with various embodiments of the invention, focal DNA amplifications in subgroups. Copy number alterations in subgroups were evaluated using GISTIC and the q score for statistically significant focal DNA copy number gains (q score<0.25) listed. Focal copy number changes common to all subgroups (q<0.25 in all subgroups) are not reported.

FIG. 15 depicts, in accordance with various embodiments of the invention, focal DNA deletions in subgroups. Copy number alterations in subgroups were evaluated using GISTIC and the q score for statistically significant focal DNA copy number losses (q score<0.25) are listed. Focal copy number changes common to all subgroups (q<0.25 in all subgroups) are not reported.

FIGS. 16A-16B depict, in accordance with various embodiments of the invention, median expression values of AKT pathway genes in each AKT cancer subgroup in the discovery dataset corresponding to the heatmap in FIG. 10.

FIG. 17 depicts, in accordance with various embodiments of the invention, evidence that Mesenchymal patients benefit from temozolomide. Kaplan Meier survival curves were plotted within each subgroup for TCGA patients receiving more (≥3 cycles; red) vs. less (<3 cycles; black) temozolomide. Only Mesenchymal patients had a statistically significant difference in survival between treatment arms. Median survival was 0.6 years greater for Mesenchymal patients treated with more temozolomide (1.8 years) vs. less temozolomide (1.2 years); p=0.01 log rank; not age adjusted.

FIGS. 18A-18C depict, in accordance with an embodiment herein, a plot of correlations between clustered samples. (FIG. 18A) Expression profiling of 14 non-neoplastic autopsy specimens from donors with no history of brain tumor or neurological disorder and 181 HGG was performed using Affymetrix U133A and U133B chips on tumors collected at UCSF, MDA, and UCLA (GSE4271 and GSE4412). A sample correlation cluster map was generated using a hand curated list of Akt pathway genes. (FIG. 18B) Kaplan Meier curves for tumors in clusters 1 through 5 and non-clustering tumors. (FIG. 18C) Differences in Kaplan Meier survival curves for patients in subgroups 4 and 5 approach significance; p=0.06 (log rank). Results: There are 5 subgroups of HGG patients that have different expression of Akt pathway genes and different survival curves. There are 3 well defined clusters of tumors (yellow arrows), 2 less defined clusters (pink arrows), and a group of genes (lower left) that are not part of well-defined clusters (cluster 0).

FIGS. 19A-19D depict, in accordance with an embodiment herein, GBM tumors cluster into distinct subtypes based on expression of PI3K/Akt pathway genes. Expression profiling was as described in FIGS. 18A-18C herein. Two way unsupervised hierarchical clustering was performed using Pearson/centroid metric/linkages for PI3K/Akt pathway genes in all tumors and non-neoplastic brain. Cluster numbers 1-5 (labeled at the bottom) contain tumors identified from the plot of correlations between clustered samples shown in FIGS. 18A-18C. Results: PDGFRα is overexpressed in subgroup 4 and EGFR in subgroup 3, among other results.

FIGS. 20A-20D depict, in accordance with an embodiment herein, Akt subgroups in GBM. Correlation map generated using Akt pathway genes and GSE4271 (expression profiling results from 171 WHO grade IV astrocytoma and 14 non-neoplastic controls from autopsy). Map generated with a custom program implemented in R (FIGS. 20A-20B). Similar results were obtained using the TCGA dataset (FIGS. 20B-20C). Kaplan Meyer curves are plotted for patient subgroups. Results: There are 5 patient subgroups that have different patterns of Akt pathway gene expression. Differences in survival for patients in clusters 4 and 5 in FIGS. 20A-20B approached significance p=0.06 (log rank).

FIG. 21 depicts, in accordance with an embodiment herein, recurrent tumors fall in subgroups 0, 3, 4 and 5. Recurrent tumors in the correlation plot from FIG. 20A are marked with arrows.

FIGS. 22A-22C depict distribution of Akt pathway genes in subgroups. Two-way unsupervised hierarchical clustering was performed using Pearson/Centroid metric/linkages for Akt pathway genes in GSE4271 with non-clustering tumors removed. Tumors in clusters 1-5 correspond to clusters in FIGS. 20A-20D.

FIG. 23 (prior art) depicts a schematic representation of the Akt pathway.

FIGS. 24A-24B depict, in accordance with an embodiment herein, human-rodent xenograft models of Akt subgroups associated with TMZ sensitivity. The inventors analyzed replicates of 15 xenografts and 1 human cell line for Akt classes. Mean survival for placebo, temodar (TMZ), radiation (RT) or concurrent TMZ+RT treated mice in each subgroup (FIG. 24B). Significance determined with a 2-sample, 2-sided t test assuming unequal variance. Intracranial xenografts are prepared from flank passaged GBM tissue.

DETAILED DESCRIPTION OF THE INVENTION

All references cited herein are incorporated by reference in their entirety as though fully set forth. Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Allen et al., Remington: The Science and Practice of Pharmacy 22^(nd) ed., Pharmaceutical Press (Sep. 15, 2012); Hornyak et al., Introduction to Nanoscience and Nanotechnology, CRC Press (2008); Singleton and Sainsbury, Dictionary of Microbiology and Molecular Biology 3^(rd) ed., revised ed., J. Wiley & Sons (New York, N.Y. 2006); Smith, March's Advanced Organic Chemistry Reactions, Mechanisms and Structure 7^(th) ed., J. Wiley & Sons (New York, N.Y. 2013); Singleton, Dictionary of DNA and Genome Technology 3^(rd) ed., Wiley-Blackwell (Nov. 28, 2012); and Green and Sambrook, Molecular Cloning: A Laboratory Manual 4th ed., Cold Spring Harbor Laboratory Press (Cold Spring Harbor, N.Y. 2012), provide one skilled in the art with a general guide to many of the terms used in the present application. For references on how to prepare antibodies, see Greenfield, Antibodies A Laboratory Manual 2^(nd) ed., Cold Spring Harbor Press (Cold Spring Harbor N.Y., 2013); Köhler and Milstein, Derivation of specific antibody-producing tissue culture and tumor lines by cell fusion, Eur. J. Immunol. 1976 July, 6(7):511-9; Queen and Selick, Humanized immunoglobulins, U.S. Pat. No. 5,585,089 (1996 December); and Riechmann et al., Reshaping human antibodies for therapy, Nature 1988 Mar. 24, 332(6162):323-7.

One skilled in the art will recognize many methods and materials similar or equivalent to those described herein, which could be used in the practice of the present invention. Other features and advantages of the invention will become apparent from the following detailed description, taken in conjunction with the accompanying drawings, which illustrate, by way of example, various features of embodiments of the invention. Indeed, the present invention is in no way limited to the methods and materials described. For convenience, certain terms employed herein, in the specification, examples and appended claims are collected here.

Unless stated otherwise, or implicit from context, the following terms and phrases include the meanings provided below. Unless explicitly stated otherwise, or apparent from context, the terms and phrases below do not exclude the meaning that the term or phrase has acquired in the art to which it pertains. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. It should be understood that this invention is not limited to the particular methodology, protocols, and reagents, etc., described herein and as such can vary. The definitions and terminology used herein are provided to aid in describing particular embodiments, and are not intended to limit the claimed invention, because the scope of the invention is limited only by the claims.

As used herein the term “comprising” or “comprises” is used in reference to compositions, methods, and respective component(s) thereof, that are useful to an embodiment, yet open to the inclusion of unspecified elements, whether useful or not. It will be understood by those within the art that, in general, terms used herein are generally intended as “open” terms (e.g., the term “including” should be interpreted as “including but not limited to,” the term “having” should be interpreted as “having at least,” the term “includes” should be interpreted as “includes but is not limited to,” etc.).

Unless stated otherwise, the terms “a” and “an” and “the” and similar references used in the context of describing a particular embodiment of the application (especially in the context of claims) can be construed to cover both the singular and the plural. The recitation of ranges of values herein is merely intended to serve as a shorthand method of referring individually to each separate value falling within the range. Unless otherwise indicated herein, each individual value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (for example, “such as”) provided with respect to certain embodiments herein is intended merely to better illuminate the application and does not pose a limitation on the scope of the application otherwise claimed. The abbreviation, “e.g.” is derived from the Latin exempli gratia, and is used herein to indicate a non-limiting example. Thus, the abbreviation “e.g.” is synonymous with the term “for example.” No language in the specification should be construed as indicating any non-claimed element essential to the practice of the application.

As used herein, the terms “treat,” “treatment,” “treating,” or “amelioration” when used in reference to a disease, disorder or medical condition, refer to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent, reverse, alleviate, ameliorate, inhibit, lessen, slow down or stop the progression or severity of a symptom or condition. The term “treating” includes reducing or alleviating at least one adverse effect or symptom of a condition. Treatment is generally “effective” if one or more symptoms or clinical markers are reduced. Alternatively, treatment is “effective” if the progression of a disease, disorder or medical condition is reduced or halted. That is, “treatment” includes not just the improvement of symptoms or markers, but also a cessation or at least slowing of progress or worsening of symptoms that would be expected in the absence of treatment. Also, “treatment” may mean to pursue or obtain beneficial results, or lower the chances of the individual developing the condition even if the treatment is ultimately unsuccessful. Those in need of treatment include those already with the condition as well as those prone to have the condition or those in whom the condition is to be prevented.

“Beneficial results” or “desired results” may include, but are in no way limited to, lessening or alleviating the severity of the disease condition, preventing the disease condition from worsening, curing the disease condition, preventing the disease condition from developing, lowering the chances of a patient developing the disease condition, decreasing morbidity and mortality, and prolonging a patient's life or life expectancy. As non-limiting examples, “beneficial results” or “desired results” may be alleviation of one or more symptom(s), diminishment of extent of the deficit, stabilized (i.e., not worsening) state of a tumor, delay or slowing of a tumor, and amelioration or palliation of symptoms associated with a tumor.

“Disorders”, “diseases”, “conditions” and “disease conditions,” as used herein may include, but are in no way limited to any form of malignant neoplastic cell proliferative disorders or diseases. Examples of such disorders include but are not limited to cancer and tumor.

A “cancer” or “tumor” as used herein refers to an uncontrolled growth of cells which interferes with the normal functioning of the bodily organs and systems, and/or all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues. A subject that has a cancer or a tumor is a subject having objectively measurable cancer cells present in the subject's body. Included in this definition are benign and malignant cancers, as well as dormant tumors or micrometastasis. Cancers which migrate from their original location and seed vital organs can eventually lead to the death of the subject through the functional deterioration of the affected organs. As used herein, the term “invasive” refers to the ability to infiltrate and destroy surrounding tissue. Examples of cancer include, but are not limited to, nervous system tumor, nerve sheath tumor, and brain tumor or cancer. Examples of brain tumor include, but are not limited to, benign brain tumor, malignant brain tumor, primary brain tumor, secondary brain tumor, metastatic brain tumor, glioma, glioblastoma, glioblastoma multiforme (GBM), medulloblastoma, ependymoma, astrocytoma, pilocytic astrocytoma, oligodendroglioma, brainstem glioma, optic nerve glioma, mixed glioma such as oligoastrocytoma, low-grade glioma, high-grade glioma, supratentorial glioma, infratentorial glioma, pontine glioma, meningioma, pituitary adenoma, and nerve sheath tumor. Nervous system tumor or nervous system neoplasm refers to any tumor affecting the nervous system. A nervous system tumor can be a tumor in the central nervous system (CNS), in the peripheral nervous system (PNS), or in both CNS and PNS. Examples of nervous system tumor include but are not limited to brain tumor, nerve sheath tumor, and optic nerve glioma.

As used herein, the term “administering,” refers to the placement an agent as disclosed herein into a subject by a method or route which results in at least partial localization of the agents at a desired site. “Route of administration” may refer to any administration pathway known in the art, including but not limited to aerosol, nasal, oral, transmucosal, transdermal, parenteral, enteral, topical or local. “Parenteral” refers to a route of administration that is generally associated with injection, including intracranial, intraventricular, intrathecal, epidural, intradural, intraorbital, infusion, intraarterial, intracapsular, intracardiac, intradermal, intramuscular, intraperitoneal, intrapulmonary, intraspinal, intrasternal, intrathecal, intrauterine, intravenous, subarachnoid, subcapsular, subcutaneous, transmucosal, or transtracheal. Via the parenteral route, the compositions may be in the form of solutions or suspensions for infusion or for injection, or as lyophilized powders. Via the enteral route, the pharmaceutical compositions can be in the form of tablets, gel capsules, sugar-coated tablets, syrups, suspensions, solutions, powders, granules, emulsions, microspheres or nanospheres or lipid vesicles or polymer vesicles allowing controlled release. Via the topical route, the pharmaceutical compositions can be in the form of aerosol, lotion, cream, gel, ointment, suspensions, solutions or emulsions. In accordance with the present invention, “administering” can be self-administering. For example, it is considered as “administering” that a subject consumes a composition as disclosed herein.

The term “sample” or “biological sample” as used herein denotes a sample taken or isolated from a biological organism, e.g., a tumor sample from a subject. Exemplary biological samples include, but are not limited to, cheek swab; mucus; whole blood, blood, serum; plasma; urine; saliva; semen; lymph; fecal extract; sputum; other body fluid or biofluid; cell sample; tissue sample; tumor sample; and/or tumor biopsy etc. The term also includes a mixture of the above-mentioned samples. The term “sample” also includes untreated or pretreated (or preprocessed) biological samples. In some embodiments, a sample can comprise one or more cells from the subject. In some embodiments, a sample can be a tumor cell sample, e.g. the sample can comprise cancerous cells, cells from a tumor, and/or a tumor biopsy.

As used herein, a “subject” means a human or animal. Usually the animal is a vertebrate such as a primate, rodent, domestic animal or game animal. Primates include chimpanzees, cynomologous monkeys, spider monkeys, and macaques, e.g., Rhesus. Rodents include mice, rats, woodchucks, ferrets, rabbits and hamsters. Domestic and game animals include cows, horses, pigs, deer, bison, buffalo, feline species, e.g., domestic cat, and canine species, e.g., dog, fox, wolf. The terms, “patient”, “individual” and “subject” are used interchangeably herein. In an embodiment, the subject is mammal. The mammal can be a human, non-human primate, mouse, rat, dog, cat, horse, or cow, but are not limited to these examples. In addition, the methods described herein can be used to treat domesticated animals and/or pets.

“Mammal” as used herein refers to any member of the class Mammalia, including, without limitation, humans and nonhuman primates such as chimpanzees and other apes and monkey species; farm animals such as cattle, sheep, pigs, goats and horses; domestic mammals such as dogs and cats; laboratory animals including rodents such as mice, rats and guinea pigs, and the like. The term does not denote a particular age or sex. Thus, adult and newborn subjects, as well as fetuses, whether male or female, are intended to be included within the scope of this term.

A subject can be one who has been previously diagnosed with or identified as suffering from or having a condition in need of treatment (e.g., GBM) or one or more complications related to the condition, and optionally, have already undergone treatment for the condition or the one or more complications related to the condition. Alternatively, a subject can also be one who has not been previously diagnosed as having a condition or one or more complications related to the condition. For example, a subject can be one who exhibits one or more risk factors for a condition or one or more complications related to the condition or a subject who does not exhibit risk factors. A “subject in need” of treatment for a particular condition can be a subject suspected of having that condition, diagnosed as having that condition, already treated or being treated for that condition, not treated for that condition, or at risk of developing that condition.

The term “statistically significant” or “significantly” refers to statistical evidence that there is a difference. It is defined as the probability of making a decision to reject the null hypothesis when the null hypothesis is actually true. The decision is often made using the p-value.

As used herein, “variants” can include, but are not limited to, those that include conservative amino acid mutations, SNP variants, splicing variants, degenerate variants, and biologically active portions of a gene. A “degenerate variant” as used herein refers to a variant that has a mutated nucleotide sequence, but still encodes the same polypeptide due to the redundancy of the genetic code.

The term “functional” when used in conjunction with “equivalent”, “analog”, “derivative” or “variant” or “fragment” refers to an entity or molecule which possess a biological activity that is substantially similar to a biological activity of the entity or molecule of which it is an equivalent, analog, derivative, variant or fragment thereof.

As used herein, the term “alkylating agents” refers to compounds and molecules used in cancer treatment that attach an alkyl group (C_(n)H_(2n)+1) to DNA. Examples of alkylating agents include but are not limited to nitrogen mustards such as cyclophosphamide, mechlorethamine or mustine (HN2), uramustine or uracil mustard, melphalan, chlorambucil, ifosfamide, and bendamustine; nitrosoureas such as carmustine (BCNU), lomustine (CCNU), and streptozocinm; alkyl sulfonates such busulfan; thiotepa; and temozolomide; and these alkylating agents' analogs, derivative, and salts.

As used herein, the term “PI3K/AKT/mTOR inhibitor” (also interchangeably called as PI3K/AKT/mTOR blocker, anti-PI3K/AKT/mTOR reagent, agent, drug or therapeutic,) refers to any reagent that inhibits the PI3K/AKT/mTOR signaling, including inhibition of any molecular signaling steps upstream or downstream of PI3K/AKT/mTOR. A PI3K/AKT/mTOR inhibitor can be a small molecule; a nucleic acid such as siRNA, shRNA, and miRNA; a nucleic acid analogue such as PNA, pc-PNA, and LNA; an aptamer; a ribosome; a peptide; a protein; an avimer; an antibody, or variants and fragments thereof. Examples of the PI3K/AKT/mTOR inhibitor include but are not limited to wortmannin, demethoxyviridin, LY294002, perifosine, idelalisib, PX-866, IPI-145, BAY 80-6946, BEZ235, RP6530, TGR 1202, SF1126, INK1117, GDC-0941, BKM120, XL147 (also known as SAR245408), XL765 (also known as SAR245409), Palomid, GSK1059615, ZSTK474, PWT33597, IC87114, TG100-115, CAL263, RP6503, PI-103, GNE-477, CUDC-907, and AEZS-136; VQD-002, miltefosine, and AZD5363; rapamycin, temsirolimus, evirolimus, ridaforolimus, epigallocatechin gallate (EGCG), caffeine, curcumin, and resveratrol.

As used herein, the term “IDH” means isocitrate dehydrogenase. SEQ ID NO:1 sets forth one non-limiting example of an IDH1 gene sequence. As further disclosed herein, to characterize subgroups, the inventors found the distribution for alterations in glioma-associated genes in subgroups. It was found that subgroup 5 was enriched in tumors with IDH mutations. For example, IDH mutations in glioma may be found at arginine 132 (R132) residue of isocitrate dehydrogenase I (IDH1) or the R172 residue of IDH2. SEQ ID NO:2 sets forth one non-limiting example of an IDH1 sequence, that is, the cDNA sequence of one variant of IDH1. SEQ ID NO:3 sets forth another non-limiting example of an IDH1 sequence, that is, the cDNA sequence of another variant of IDH1. SEQ ID NO:4 sets forth one non-limiting example of an IDH2 gene sequence.

For cancers such as GBM, many ineffective therapies can result from classifying the disease too generally. However, variations in natural history and therapeutic response, as well as molecular profiling, suggest that there could be molecular subtypes beyond the standard classifications. The ramifications are not insignificant. For example, the failure to classify GBM subtypes can affect patient treatment, drug development and clinical trials. Clinical trials that do not stratify for subgroups are underpowered and could miss subtype-specific drugs. Furthermore, unstratified patients may bear extra expense and toxicity. Targets within a subgroup might be missed if GBM are considered as a whole. The PI3K/Akt pathway is one of the 3 core pathways consistently altered in GBM. It often leads to activation of Akt. Akt is an oncogenic serine/threonine kinase that regulates metabolism, survival, autophagy, proliferation, migration, epithelial to mesenchymal (EMT) transition and angiogenesis. The pathway is a large and complex with many regulators, activators, effectors and feedback loops.

As disclosed herein, the inventors investigated PI3K/Akt/mTOR signaling variations in Akt subgroups, providing therapeutic alternatives for glioblastoma. The GFR/PI3K/Akt pathway is an important therapeutic target in glioblastoma (GB), but in the past, response to pathway inhibitors in clinical trials has been lackluster. The inventors examined whether AKT pathway variations contribute to poor response, and classified GBM based on AKT pathway genes. There were at least 5 GBM AKT subgroups. They were concordant with other found subgroups but subdivided them further to give new groups with distinct features. AKT subgroups had different molecular alterations and median survival. Importantly, the results demonstrated that there is a subset of GB patients sensitive to alkylating agent, and AKT classification can identify them. Akt classification also identified two subgroups enriched in IDH1 mutations with different clinical courses and molecular alterations. To characterize subgroups, the inventor found the distribution for alterations in glioma-associated genes in subgroups, and found subgroup 5 was enriched in tumors with IDH1 mutations. These data suggest AKT classification is a biomarker for sensitivity to alkylating agents and PI3K/AKT pathway inhibitors. The results advance molecular classification of GB and can be used to stratify patients for clinical trials and enhance discovery of class-specific therapeutic targets.

As further disclosed herein, it was found that there was a statistically significant enrichment of IDH1 mutations in the AKT subgroup 5 cluster. Many IDH mutations in glioma are found at arginine 132 (R132) residue of isocitrate dehydrogenase I (IDH1) or the R172 residue of IDH2. There was also evidence found that the AKT subgroup 5 patients as described herein were particularly sensitive to alkylating agents.

In another embodiment, the present invention provides a method of diagnosing a cancer subtype in a subject comprising obtaining a sample from the subject, assaying the sample to determine an AKT expression profile, and diagnosing the cancer subtype based on the AKT expression profile. In another embodiment, the cancer is GBM. In another embodiment, the subject is human. In another embodiment, the subtype is characterized by a cluster defined by the distribution of alterations in glioma associated genes. In one embodiment, the AKT expression profile is defined by a cluster of distribution of alterations in glioma associated genes in the AKT signaling pathway. In one embodiment, wherein the AKT expression profile is made up of one or more genetic loci listed in Table 2, Table 4, Table 5, or Table 6. In one embodiment, the cancer subtype is a cancer subtype of GBM. In one embodiment, the cancer subtype includes the presence of tumors enriched with one or more IDH1 and/or IDH2 mutations.

In one embodiment, the present invention provides a method of diagnosing a cancer subtype in a subject comprising obtaining a sample from the subject, assaying the sample to determine the presence or absence of IDH1 and/or IDH2 mutations, and diagnosing the cancer subtype based on the presence of IDH1 and/or IDH2 mutations. In another embodiment, the cancer is GBM. In one embodiment, the individual is a human. In another embodiment, the presence of one or more IDH1 and/or IDH2 mutations relative to a normal individual is indicative of the cancer subtype AKT subgroup 5.

In another embodiment, the present invention provides a method of prognosing GBM disease by diagnosing a GBM disease subtype based on the AKT expression profile, and determining the severity of the disease based on the GBM disease subtype.

In one embodiment, the present invention provides for a method of treating a subject for cancer comprising obtaining a sample from the subject, assaying the sample to determine a cancer subtype based on what is the AKT expression profile, and treating the subject. In another embodiment, the cancer is GBM. In another embodiment, the subject is human. In another embodiment, the subtype is characterized by a cluster defined by the distribution of alterations in glioma associated genes. In another embodiment, the treatment comprises administering a therapeutically effective dosage of a composition comprising one or more alkylating agents to the individual. In another embodiment, the treatment comprises administering a therapeutically effective dosage of a composition comprising one or more PI3K/Akt/mTOR inhibitors to the individual.

In one embodiment, the present invention provides for a method of treating GBM in a subject comprising obtaining a sample from the subject, assaying the sample to diagnose a GBM subtype based on the presence of an AKT expression profile, and treating the subject. In some embodiments, the AKT subgroup includes the presence of one or more IDH1 and/or IDH2 mutations. In another embodiment, the present invention provides a method of treating an individual for cancer by obtaining a sample from the individual, assaying the sample to determine the presence of one or more IDH1 and/or IDH2 mutations, and treating the individual. In another embodiment, treating the individual comprises administration of a therapeutically effective dosage of a composition comprising one or more alkylating agents to the individual.

In various embodiments, the one or more IDH1 mutations include mutation of arginine 132 (R132) residue of isocitrate dehydrogenase I (IDH1). In various embodiments, the one or more IDH2 mutations include the mutation of arginine 172 (R172) residue of IDH2. In various embodiments, assaying the sample includes determining the presence of a GBM tumor enriched with one or more IDH1 and/or IDH2 mutations.

Activity of GFR/PI3K/AKT pathway inhibitors in glioblastoma clinical trials has not been robust. While not wishing to be bound by any theory, the inventors believe that variations in the pathway between tumors contribute to poor response. The inventors clustered GBM based on AKT pathway genes and discovered new subtypes then characterized their clinical and molecular features. There are at least 5 GBM AKT subtypes having distinct DNA copy number alterations, enrichment in oncogenes and tumor suppressor genes and patterns of expression for PI3K/AKT/mTOR signaling components. Gene Ontology terms indicate a different cell of origin or dominant phenotype for each subgroup. Evidence suggests one subtype is very sensitive to BCNU or CCNU (median survival 5.8 vs. 1.5 years; BCNU/CCNU vs other treatments; respectively). AKT subtyping advances previous approaches by revealing additional subgroups with unique clinical and molecular features. Evidence indicates it is a predictive marker for response to BCNU or CCNU and PI3K/AKT/mTOR pathway inhibitors. The inventors demonstrate that Akt subtyping helps stratify patients for clinical trials and augments discovery of class-specific therapeutic targets.

Classification and Diagnosis Methods

In various embodiments, the present invention provides a method for categorizing/classifying/stratifying a subject with a cancer into a subgroup. The method may consist of, or may consist essentially of, or may comprise: obtaining a sample from the subject; assaying the sample to detect increases and/or decreases in expression levels of AKT pathway components relative to reference samples or values; detecting the subgroup's expression pattern of AKT pathway components in the sample based on the detected increases and/or decreases; and categorizing/classifying/stratifying the subject having the subgroup's expression pattern of AKT pathway components into the subgroup. In various embodiments, the AKT pathway components comprise one, two, three, four, five, six, or more, or all genes listed Table 2, and/or Table 4, and/or Table 5, and/or Table 6.

In various embodiments, the subgroup is C1, PN, MES, CLAS, SL, or PROLIF. In various embodiments, categorizing/classifying/stratifying comprises categorizing/classifying/stratifying the subject having subgroup C1's expression pattern of AKT pathway components into subgroup C1, the subject having subgroup PN's expression pattern of AKT pathway components into subgroup PN, the subject having subgroup MES's expression pattern of AKT pathway components into subgroup MES, the subject having subgroup CLAS's expression pattern of AKT pathway components into subgroup CLAS, the subject having subgroup SL's expression pattern of AKT pathway components into subgroup SL, or the subject having subgroup PROLIF's expression pattern of AKT pathway components into subgroup PROLIF.

FIGS. 6A-6B, 7A-7B, 10 and 16A-B illustrate non-limiting examples of subgroup C1's expression pattern of AKT pathway components, subgroup PN's expression pattern of AKT pathway components, subgroup MES's expression pattern of AKT pathway components, subgroup CLAS's expression pattern of AKT pathway components, subgroup SL's expression pattern of AKT pathway components, and subgroup PROLIF's expression pattern of AKT pathway components.

In some embodiments, in FIGS. 16A-16B, values not less than 0.05 may be considered as increased expression; values not more than −0.05 may be considered as decreased expression; and values between 0.05 and −0.05 may be considered as insignificantly changed expression.

For non-limiting examples, subgroup C1's expression pattern of AKT pathway components may comprise increased expression levels in one or more of ATXN1, BCL10, CDKN1B, CFD, CHEK1, EIF3E, EIF3H, EPAS1, EZH2, FOXO3, HIF1A, HSP90B1, IRS1, IRS2, KRAS, MAP3K5, NRAS, PALLD, PDGFA, PDGFC, PDGFD, PDK1, PIK3CA, PIK3R1, PKD2, PKN2, PPARGC1A, PPP2R2B, SRSF1, SSB, SYK, TWIST1, and WNK1; and/or insignificantly changed expression levels in one or more of CCND1, CDKN1A, KDR, TRIB3, and VIM; and/or decreased expression levels in one or more of ACLY, AKT1, CDC37, EGFR, EIF3B, EIF3G, EIF4EBP1, FGFR2, FGFR3, FYN, GAB1, GAB2, GRB10, GSK3B, HSP90AB1, INPP5D, MAPK8IP1, PDGFRB, PHLPP1, PIK3C2B, PPP2R1A, RAF1, SORBS2, TP53, TSC1, and TSC2.

For non-limiting examples, subgroup PN's expression pattern of AKT pathway components may comprise increased expression levels in one or more of ATXN1, FGFR2, FGFR3, GAB2, GSK3B, HSP90AB1, IRS1, KRAS, MAP3K5, MAPK8IP1, PHLPP1, PIK3C2B, PIK3R1, PPARGC1A, PPP2R1A, PPP2R2B, SORBS2, TSC1, and TSC2; and/or insignificantly changed expression levels in one or more of CDKN1B, CFD, EPAS1, FOXO3, GAB1, KDR, and WNK1; and/or decreased expression levels in one or more of ACLY, AKT1, BCL10, CCND1, CDC37, CDKN1A, CHEK1, EGFR, EIF3B, EIF3E, EIF3G, EIF3H, EIF4EBP1, EZH2, FYN, GRB10, HIF1A, HSP90B1, INPP5D, IRS2, NRAS, PALLD, PDGFA, PDGFC, PDGFD, PDGFRB, PDK1, PIK3CA, PKD2, PKN2, RAF1, SRSF1, SSB, SYK, TP53, TRIB3, TWIST1, and VIM.

For non-limiting examples, subgroup MES's expression pattern of AKT pathway components may comprise increased expression levels in one or more of AKT1, BCL10, CCND1, CDC37, CDKN1A, CFD, EIF3B, EPAS1, GRB10, HIF1A, HSP90B1, INPP5D, IRS1, IRS2, KDR, PALLD, PDGFA, PDGFC, PDGFD, PDGFRB, PDK1, PKD2, SYK, TRIB3, TWIST1, and VIM; and/or insignificantly changed expression levels in one or more of CHEK1, EIF3G, EIF4EBP1, MAP3K5, PKN2, SORBS2, TP53, and WNK1; and/or decreased expression levels in one or more of ACLY, ATXN1, CDKN1B, EGFR, EIF3E, EIF3H, EZH2, FGFR2, FGFR3, FOXO3, FYN, GAB1, GAB2, GSK3B, HSP90AB1, KRAS, MAPK8IP1, NRAS, PHLPP1, PIK3C2B, PIK3CA, PIK3R1, PPARGC1A, PPP2R1A, PPP2R2B, RAF1, SRSF1, SSB, TSC1, and TSC2.

For non-limiting examples, subgroup CLAS's expression pattern of AKT pathway components may comprise increased expression levels in one or more of ACLY, AKT1, CDC37, CDKN1A, CHEK1, EGFR, EIF3B, EIF3E, EIF3G, EIF4EBP1, EPAS1, FGFR3, FYN, GAB1, GRB10, HIF1A, HSP90B1, IRS2, KDR, MAPK8IP1, NRAS, PALLD, PDGFA, PDGFC, PDGFD, PDGFRB, PDK1, PKD2, PKN2, PPARGC1A, PPP2R1A, PPP2R2B, RAF1, SRSF1, SSB, TP53, TRIB3, TWIST1, and VIM; and/or insignificantly changed expression levels in one or more of ATXN1, BCL10, EIF3H, EZH2, HSP90AB1, INPP5D, PIK3R1, and SYK; and/or decreased expression levels in one or more of CCND1, CDKN1B, CFD, FGFR2, FOXO3, GAB2, GSK3B, IRS1, KRAS, MAP3K5, PHLPP1, PIK3C2B, PIK3CA, SORBS2, TSC1, TSC2, and WNK1.

For non-limiting examples, subgroup SL's expression pattern of AKT pathway components may comprise increased expression levels in one or more of ACLY, CCND1, CDKN1B, EGFR, EIF3B, EIF3E, EIF3G, EIF3H, FOXO3, FYN, GAB1, GAB2, INPP5D, IRS1, MAP3K5, MAPK8IP1, PDGFC, PHLPP1, PIK3C2B, PIK3CA, PIK3R1, RAF1, SYK, TP53, TRIB3, TSC1, and TSC2; and/or insignificantly changed expression levels in one or more of ATXN1, CDC37, GSK3B, HSP90AB1, PKN2, PPP2R2B, and SRSF1; and/or decreased expression levels in one or more of AKT1, BCL10, CDKN1A, CFD, CHEK1, EIF4EBP1, EPAS1, EZH2, FGFR2, FGFR3, GRB10, HIF1A, HSP90B1, IRS2, KDR, KRAS, NRAS, PALLD, PDGFA, PDGFD, PDGFRB, PDK1, PKD2, PPARGC1A, PPP2R1A, SORBS2, SSB, TWIST1, VIM, and WNK1.

For non-limiting examples, subgroup PROLIF's expression pattern of AKT pathway components may comprise increased expression levels in one or more of ACLY, AKT1, BCL10, CCND1, CDKN1B, CHEK1, EIF3B, EIF3E, EIF3G, EIF3H, EIF4EBP1, EZH2, FYN, GSK3B, HSP90AB1, HSP90B1, NRAS, PDK1, PIK3CA, PPP2R1A, RAF1, SRSF1, SSB, TP53, TRIB3, TSC2, and TWIST1; and/or insignificantly changed expression levels in one or more of CDC37, GAB1, GRB10, IRS1, KRAS, PHLPP1, PKN2, and VIM; and/or decreased expression levels in one or more of ATXN1, CDKN1A, CFD, EGFR, EPAS1, FGFR2, FGFR3, FOXO3, GAB2, HIF1A, INPP5D, IRS2, KDR, MAP3K5, MAPK8IP1, PALLD, PDGFA, PDGFC, PDGFD, PDGFRB, PIK3C2B, PIK3R1, PKD2, PPARGC1A, PPP2R2B, SORBS2, SYK, TSC1, and WNK1.

In various embodiments, the subgroup is subgroup 0, subgroup 1, subgroup 2, subgroup 3, subgroup 4, or subgroup 5. In various embodiments, categorizing/classifying/stratifying comprises categorizing/classifying/stratifying the subject having subgroup 0's expression pattern of AKT pathway components into subgroup 0, categorizing/classifying/stratifying the subject having subgroup 1's expression pattern of AKT pathway components into subgroup 1, the subject having subgroup 2's expression pattern of AKT pathway components into subgroup 2, the subject having subgroup 3's expression pattern of AKT pathway components into subgroup 3, the subject having subgroup 4's expression pattern of AKT pathway components into subgroup 4, or the subject having subgroup 5's expression pattern of AKT pathway components into subgroup 5. FIGS. 19A-19D and 22A-22C illustrate non-limiting examples of subgroup 0's expression pattern of AKT pathway components, subgroup 1's expression pattern of AKT pathway components, subgroup 2's expression pattern of AKT pathway components, subgroup 3's expression pattern of AKT pathway components, subgroup 4's expression pattern of AKT pathway components, and subgroup 5's expression pattern of AKT pathway components.

In various embodiments, increases and/or decreases in expression levels of AKT pathway components relative to reference samples or values are detected by: contacting the sample with detection agents that specifically bind to AKT pathway components; and detecting the binding levels between the detection agents and the AKT pathway components. In various embodiments, increases and/or decreases in expression levels of AKT pathway components relative to reference samples or values are detected by using a microarray.

In various embodiments, the sample is assayed to detect increases or decreases in mRNA expression levels of one or more genes listed Table 2, Table 4, Table 5, or Table 6 relative to reference samples or values. In various embodiments, the sample is assayed to detect increases or decreases in protein expression levels of one or more genes listed Table 2, Table 4, Table 5, or Table 6 relative to reference samples or values.

In various embodiments, the reference sample is a non-neoplastic sample. In various embodiments, the non-neoplastic sample is obtained from an individual without a brain tumor or a neurological disorder. In various embodiments, the individual and the subject belong to the same species, for example, human. In various embodiments, the reference value is obtained from one or more non-neoplastic samples.

In various embodiments, the present invention provides a method for categorizing/classifying/stratifying a cancer in a subject. The method may consist of or may consist essentially of or may comprise: obtaining a biological sample from the subject; determining an expression pattern of AKT pathway components in the biological sample; and categorizing/classifying/stratifying the cancer based on the determined expression pattern of AKT pathway components in the biological sample. In various embodiments, said classifying comprises categorizing/classifying/stratifying the cancer into C1, PN, MES, CLAS, SL, or PROLIF subtype if the biological sample's expression pattern of AKT pathway components is determined to be C1, PN, MES, CLAS, SL, or PROLIF subtype's expression pattern of AKT pathway components. Non-limiting examples of C1, PN, MES, CLAS, SL, or PROLIF subtype's expression pattern of AKT pathway components may be found in FIG. 10 or Table 6.

In various embodiments, the present invention provides a method for diagnosing whether a subject has a cancer subtype. The method may consist of or may consist essentially of or may comprise: obtaining a biological sample from the subject; determining whether the cancer subtype's expression pattern of AKT pathway components is present in the biological sample; and diagnosing the subject as having the cancer subtype after the cancer subtype's expression pattern of AKT pathway components is determined to be present in the biological sample. In various further embodiments, the method comprises administering a therapeutically effective amount of a therapeutic to the subject, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of the cancer subtype. In some embodiments, the cancer subtype is C1, PN, MES, CLAS, SL, or PROLIF subtype. In various embodiments, the expression pattern is C1, PN, MES, CLAS, SL, or PROLIF subtype's expression pattern of AKT pathway components.

In various embodiments, the cancer is a brain tumor, glioma, high grade glioma (HGG), glioblastoma, or glioblastoma multiforme (GBM). In various embodiments, the subject is a human. In various embodiments, the subject is a mammalian subject including but not limited to human, monkey, ape, dog, cat, cow, horse, goat, pig, rabbit, mouse and rat. In various embodiments, the sample or biological sample is a cancer or tumor sample. In various embodiments, the sample or biological sample comprises a cell, neuron, glia, brain cell, spinal cord cell, brain neuron, brain glia, spinal cord neuron, or spinal cord glia, or a combination thereof. In some embodiments, the sample or biological sample comprises a tumor cell or tissue. In some embodiments, the sample or biological sample comprises a tumor biopsy or sample.

In various embodiments, the AKT pathway components comprise one classifier listed in Table 2, Table 4, Table 5, or Table 6. In various embodiments, the AKT pathway components comprise two classifiers listed in Table 2, Table 4, Table 5, or Table 6. In various embodiments, the AKT pathway components comprise three classifiers listed in Table 2, Table 4, Table 5, or Table 6. In various embodiments, the AKT pathway components comprise four classifiers listed in Table 2, Table 4, Table 5, or Table 6. In various embodiments, the AKT pathway components comprise five or more classifiers listed in Table 2, Table 4, Table 5, or Table 6. In various embodiments, the AKT pathway components comprise all classifiers listed in Table 2, Table 4, Table 5, or Table 6.

In various embodiments, the AKT pathway components comprise ACLY, AKT1, ATXN1, BCL10, CCND1, CDC37, CDKN1A, CDKN1B, CFD, CHEK1, EGFR, EIF3B, EIF3E, EIF3G, EIF3H, EIF4EBP1, EPAS1, EZH2, FGFR2, FGFR3, FOXO3, FYN, GAB1, GAB2, GRB10, GSK3B, HIF1A, HSP90AB1, HSP90B1, INPP5D, IRS1, IRS2, KDR, KRAS, MAP3K5, MAPK8IP1, NRAS, PALLD, PDGFA, PDGFC, PDGFD, PDGFRB, PDK1, PHLPP1, PIK3C2B, PIK3CA, PIK3R1, PKD2, PKN2, PPARGC1A, PPP2R1A, PPP2R2B, RAF1, SORBS2, SRSF1, SSB, SYK, TP53, TRIB3, TSC1, TSC2, TWIST1, VIM, and/or WNK1, or a combination thereof.

In various embodiments, said determining is performed by: contacting the biological sample with one or more detection agents that specifically bind to one or more AKT pathway components; and detecting the level of binding between the one or more detection agents and the one or more AKT pathway components. In various embodiments, said detecting is performed by using a microarray.

In some embodiments, the one or more detection agents are oligonucleotide probes, nucleic acids, DNAs, RNAs, peptides, proteins, antibodies, aptamers, or small molecules, or a combination thereof. In some embodiments, the microarray is an oligonucleotide microarray, DNA microarray, cDNA microarrays, RNA microarray, peptide microarray, protein microarray, or antibody microarray, or a combination thereof.

In various embodiments, the method further comprises selecting, choosing or prescribing a therapeutic for the subject after diagnosis. In various embodiments, the method further comprises instructing or directing the subject to receive a therapeutic after diagnosis. In various embodiments, the method further comprises administering a therapeutically effective amount of a therapeutic to the subject, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of the diagnosed cancer subtype.

Treatment Methods

In various embodiments, the present invention provides a method for treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of a cancer in a subject, comprising: obtaining a sample from the subject; assaying the sample to detect increases and/or decreases in expression levels of AKT pathway components relative to reference samples or values; detecting an expression pattern of AKT pathway components in the sample based on the detected increases and/or decreases; and administering a therapeutically effective amount of a therapeutic to the subject, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of the cancer.

In various embodiments, the AKT pathway components comprise one, two, three, four, five, six, or more, or all genes listed Table 2, and/or Table 4, and/or Table 5, and/or Table 6. In various embodiments, the AKT pathway components comprise ACLY, AKT1, ATXN1, BCL10, CCND1, CDC37, CDKN1A, CDKN1B, CFD, CHEK1, EGFR, EIF3B, EIF3E, EIF3G, EIF3H, EIF4EBP1, EPAS1, EZH2, FGFR2, FGFR3, FOXO3, FYN, GAB1, GAB2, GRB10, GSK3B, HIF1A, HSP90AB1, HSP90B1, INPP5D, IRS1, IRS2, KDR, KRAS, MAP3K5, MAPK8IP1, NRAS, PALLD, PDGFA, PDGFC, PDGFD, PDGFRB, PDK1, PHLPP1, PIK3C2B, PIK3CA, PIK3R1, PKD2, PKN2, PPARGC1A, PPP2R1A, PPP2R2B, RAF1, SORBS2, SRSF1, SSB, SYK, TP53, TRIB3, TSC1, TSC2, TWIST1, VIM, and/or WNK1, or a combination thereof.

In various embodiments, the expression pattern of AKT pathway components is C1's expression pattern of AKT pathway components, PN's expression pattern of AKT pathway components, MES's expression pattern of AKT pathway components, CLAS's expression pattern of AKT pathway components, SL's expression pattern of AKT pathway components, or PROLIF's expression pattern of AKT pathway components. In various embodiments, the expression pattern of AKT pathway components is subgroup 0's expression pattern of AKT pathway components, subgroup 1's expression pattern of AKT pathway components, subgroup 2's expression pattern of AKT pathway components, subgroup 3's expression pattern of AKT pathway components, subgroup 4's expression pattern of AKT pathway components, or subgroup 5's expression pattern of AKT pathway components. In some embodiments, the expression pattern of AKT pathway components is SL's expression pattern of AKT pathway components, and the therapeutic is BCNU or CCNU, a functional equivalent, analog, derivative or salt of BCNU or CCNU, or a combination thereof. In some embodiments, the method further comprises instructing/directing the subject not to receive or preventing the subject from receiving TMZ, or a functional equivalent, analog, derivative or salt of TMZ, wherein the expression pattern of AKT pathway components is SL's expression pattern of AKT pathway components. In some embodiments, the method further comprises not administering TMZ, or a functional equivalent, analog, derivative or salt of TMZ to the subject, wherein the expression pattern of AKT pathway components is SL's expression pattern of AKT pathway components. In some embodiments, the expression pattern of AKT pathway components is MES's expression pattern of AKT pathway components, and the therapeutic is TMZ, a functional equivalent, analog, derivative or salt of TMZ, or a combination thereof. In some embodiments, the expression pattern of AKT pathway components is subgroup 3's expression pattern of AKT pathway components, and the therapeutic is an EGFR inhibitor. In some embodiments, the expression pattern of AKT pathway components is subgroup 4's expression pattern of AKT pathway components, and the therapeutic is a PDGFRα inhibitor.

In various embodiments, the present invention provides a method of treating a subject with a cancer, comprising: providing a subject with a cancer categorized/classified/stratified into a subgroup utilizing a categorizing/classifying/stratifying method as disclosed herein; and administering to the subject a therapeutic that specifically benefits the subgroup, thereby treating the subject. In various embodiments, the present invention provides a method of treating a subject with a cancer, comprising: categorizing/classifying/stratifying a subject with a cancer into a subgroup utilizing a categorizing/classifying/stratifying method as disclosed herein; and administering to the subject a therapeutic that specifically benefits the subgroup, thereby treating the subject.

In some embodiments, the subgroup is subgroup SL, and the therapeutic is BCNU or CCNU, a functional equivalent, analog, derivative or salt of BCNU or CCNU, or a combination thereof. In some embodiments, the method further comprises instructing/directing the subject not to receive or preventing the subject from receiving TMZ, or a functional equivalent, analog, derivative or salt of TMZ, wherein the subgroup is subgroup SL. In some embodiments, the method further comprises not administering TMZ, or a functional equivalent, analog, derivative or salt of TMZ to the subject, wherein the subgroup is subgroup SL. In some embodiments, the subgroup is subgroup MES, and the therapeutic is TMZ, a functional equivalent, analog, derivative or salt of TMZ, or a combination thereof. In some embodiments, the subgroup is subgroup 3, and the therapeutic is an EGFR inhibitor. In some embodiments, the subgroup is subgroup 4, and the therapeutic is a PDGFRα inhibitor.

In various embodiments, the present invention provides a method for treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of a cancer in a subject, comprising: providing a therapeutic; and administering a therapeutically effective amount of the therapeutic to the subject, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of the cancer. In some embodiment, the method further comprises identifying that the subject has a SL subgroup/subtype cancer or a marker for the SL subgroup/subtype, wherein the therapeutic is BCNU or CCNU, a functional equivalent, analog, derivative or salt of BCNU or CCNU, or a combination thereof. In some embodiments, the method further comprises identifying that the subject has a SL subgroup/subtype cancer or a marker for the SL subgroup/subtype and preventing the subject from receiving TMZ, or a functional equivalent, analog, derivative or salt of TMZ. In some embodiments, the method further comprises identifying that the subject has a MES subgroup/subtype cancer or a marker for the MES subgroup/subtype, wherein the therapeutic is TMZ, a functional equivalent, analog, derivative or salt of TMZ, or a combination thereof.

In various embodiment, samples are assayed to detect markers for various AKT subgroups/subtypes as disclosed herein. In some embodiments, these markers are themselves AKT pathway components. In other embodiments, these markers are themselves not AKT pathway components. Non-limiting examples of markers for the SL subgroup/sutype include mutations in IDH1 and IDH2. Mutations in IDH1 and IDH2 can be detected by antibodies that specifically recognize IDH1 and IDH2 mutant proteins through various techniques such as IHC, Western blots and protein arrays, or can be detected by genotyping assays, PCR, microarray, DNA sequencing, and RNA sequencing techniques that target IDH and IDH2 genes or mRNAs. FIG. 6B shows more than 50% of SL tumors have mutant IDH1 and very few other subtypes have this mutation. As such, R132H mutant IDH1 may be detected to identify SL patients who are sensitive to nitrosoureas (e.g., BCNU and CCNU). Non-limiting examples of markers for the MES subgroup/subtype include increased expression levels of VIM, CD44, CD45, Fibronectin, Nucleostemin etc. As such, VIM, CD44, CD45, Fibronectin, and Nucleostemin may be detected to identify MES patietns who are sensitive to temozolomide. Non-limiting examples of markers for the CLAS subgroup/subtype include mutations in EGFR and CDKN2A, and copy number alterations (CNAs). Proteins of these markers can be detected by various techniques such as IHC, Western blots and protein arrays; and genes and mRNA of these makers can be detected by genotyping assays, PCR, microarray, DNA sequencing, and RNA sequencing techniques. Also, DNA copy number alterations may also assayed to detect the markers for various AKT subgroups/subtypes as disclosed herein.

In various embodiments, the present invention provides a method for treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of a cancer in a subject. comprising: obtaining a sample from the subject; assaying the sample to detect a marker for an AKT subgroup/subtype; detecting the marker for the AKT subgroup/subtype in the sample; and administering a therapeutically effective amount of a therapeutic to the subject, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of the cancer. In some embodiments, the AKT subgroup/subtype is C1, PN, MES, CLAS, SL, or PROLIF. In other embodiments, the AKT subgroup/subtype is subgroup 0, subgroup 1, subgroup 2, subgroup 3, subgroup 4, or subgroup 5.

In various embodiments, the marker for the AKT subgroup/subtype comprises one or more mutations in IDH1 and/or IDH2. In one embodiment, the marker for the AKT subgroup/subtype comprises a mutation of R132 in IDH1 including but not limited to R132H, R132C, R132G, R132S, and R132L. In another embodiment, the marker for the AKT subgroup/subtype comprises a mutation of R172 in IDH2 including but not limited to R172K. In certain embodiments, the therapeutic is BCNU or CCNU, a functional equivalent, analog, derivative or salt of BCNU or CCNU, or a combination thereof. In further embodiments, the method comprises preventing the subject from receiving TMZ, or a functional equivalent, analog, derivative or salt of TMZ.

In various embodiments, the maker for the AKT subgroup/subtype comprises an increased expression level in VIM, CD44, CD45, Fibronectin, or Nucleostemin, or a combination thereof. In certain embodiments, the therapeutic is TMZ, a functional equivalent, analog, derivative or salt of TMZ, or a combination thereof.

In various embodiments, the marker for the AKT subgroup/subtype comprises one or more mutations in EGFR and/or CDKN2A, or copy number alterations (CNAs), or combinations thereof.

In various embodiments, the present invention provides a method of treating a SL cancer by administering to the subject BCNU or CCNU, a functional equivalent, analog, derivative or salt of BCNU or CCNU, or a combination thereof. In some embodiments, the method further comprises instructing/directing the subject not to receive or preventing the subject from receiving TMZ, or a functional equivalent, analog, derivative or salt of TMZ. In some embodiments, the method further comprises not administering TMZ, or a functional equivalent, analog, derivative or salt of TMZ to the subject.

In various embodiments, the present invention provides a method of treating a MES cancer by administering to the subject TMZ, a functional equivalent, analog, derivative or salt of TMZ, or a combination thereof.

In various embodiments, the present invention provides a method of treating a subgroup 3 cancer by administering to the subject an EGFR inhibitor.

In various embodiments, the present invention provides a method of treating a subgroup 4 cancer by administering to the subject a PDGFRα inhibitor.

In various embodiments, the present invention provides a method for treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of a cancer subtype in a subject. The method may consist of or may consist essentially of or may comprise: obtaining a biological sample from the subject; determining whether the cancer subtype's expression pattern of AKT pathway components is present in the biological sample; providing a therapeutic; and administering a therapeutically effective amount of the therapeutic to the subject after the cancer subtype's expression pattern of AKT pathway components is determined to be present in the biological sample, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of the cancer subtype. In some embodiments, the cancer subtype is C1, PN, MES, CLAS, SL, or PROLIF subtype. In various embodiments, the expression pattern is C1, PN, MES, CLAS, SL, or PROLIF subtype's expression pattern of AKT pathway components. Non-limiting examples of C1, PN, MES, CLAS, SL, or PROLIF subtype's expression pattern of AKT pathway components may be found in FIG. 10 or Table 6.

In various embodiments, the present invention provides a method for treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of SL or MES cancer subtype in a subject. The method may consist of or may consist essentially of or may comprise: obtaining a biological sample from the subject; determining whether SL or MES subtype's expression pattern of AKT pathway components is present in the biological sample; providing a therapeutic; and administering a therapeutically effective amount of the therapeutic to the subject after SL or MES subtype's expression pattern of AKT pathway components is determined to be present in the biological sample, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of SL or MES cancer subtype.

In various embodiments, the present invention provides a method for treating an AKT cancer subtype in a subject. The method may consist of or may consist essentially of or may comprise: providing a therapeutic; and administering a therapeutically effective amount of the therapeutic to the subject, thereby treating the AKT cancer subtype in the subject. In some embodiments, the cancer subtype is C1, PN, MES, CLAS, SL, or PROLIF subtype.

In various embodiments, the present invention provides a method for treating SL cancer subtype in a subject. The method may consist of or may consist essentially of or may comprise: providing a therapeutic; and administering a therapeutically effective amount of the therapeutic to the subject, thereby treating SL cancer subtype in the subject. In certain embodiments, the therapeutic is BCNU or CCNU, a functional equivalent, analog, derivative or salt of BCNU or CCNU, or a combination thereof. In some embodiments, the method further comprises instructing/directing the subject not to receive or preventing the subject from receiving TMZ, or a functional equivalent, analog, derivative or salt of TMZ. In some embodiments, the method further comprises not administering TMZ or a functional equivalent, analog, derivative or salt of TMZ to the subject.

In various embodiments, the present invention provides a method for treating MES cancer subtype in a subject. The method may consist of or may consist essentially of or may comprise: providing a therapeutic; and administering a therapeutically effective amount of the therapeutic to the subject, thereby treating MES cancer subtype in the subject. In certain embodiments, the therapeutic is TMZ, a functional equivalent, analog, derivative or salt of TMZ, or a combination thereof.

In various embodiments, the present invention provides a method for treating an AKT cancer subtype in a subject. The method comprises administering a therapeutically effective amount of the therapeutic to the subject who has been diagnosed with the AKT cancer subtype, thereby treating the AKT cancer subtype in the subject. In some embodiments, the cancer subtype is C1, PN, MES, CLAS, SL, or PROLIF subtype. In some embodiments, the subject has been diagnosed with the AKT cancer subtype via methods as described in the present invention. In various embodiments, the method may further comprise providing the therapeutic.

In various embodiments, the present invention provides a method for treating SL cancer subtype in a subject. The method comprises administering a therapeutically effective amount of the therapeutic to the subject who has been diagnosed with the SL cancer subtype, thereby treating the SL cancer subtype in the subject. In some embodiments, the subject has been diagnosed with the SL cancer subtype via methods as described in the present invention. In various embodiments, the method may further comprise providing the therapeutic. In certain embodiments, the therapeutic is BCNU or CCNU, a functional equivalent, analog, derivative or salt of BCNU or CCNU, or a combination thereof. In some embodiments, the therapeutic is not TMZ or a functional equivalent, analog, derivative or salt of TMZ.

In various embodiments, the present invention provides a method for treating MES cancer subtype in a subject. The method comprises administering a therapeutically effective amount of the therapeutic to the subject who has been diagnosed with the MES cancer subtype, thereby treating the MES cancer subtype in the subject. In some embodiments, the subject has been diagnosed with the MES cancer subtype via methods as described in the present invention. In various embodiments, the method may further comprise providing the therapeutic. In certain embodiments, the therapeutic is TMZ, a functional equivalent, analog, derivative or salt of TMZ, or a combination thereof.

In various embodiments, the present invention provides a method for treating an AKT cancer subtype in a subject. The method comprises ordering a diagnostic test to determine if the subject has an AKT cancer subtype; and administering a therapeutically effective amount of the therapeutic to the subject who has been diagnosed with the AKT cancer subtype, thereby treating the AKT cancer subtype in the subject. In some embodiments, the diagnostic test is performed via methods as described in the present invention. In some embodiments, the cancer subtype is C1, PN, MES, CLAS, SL, or PROLIF subtype. In various embodiments, the method may further comprise providing the therapeutic.

In various embodiments, the present invention provides a method for treating SL cancer subtype in a subject. The method comprises ordering a diagnostic test to determine if the subject has SL cancer subtype; and administering a therapeutically effective amount of the therapeutic to the subject who has been diagnosed with the SL cancer subtype, thereby treating the SL cancer subtype in the subject. In some embodiments, the diagnostic test is performed via methods as described in the present invention. In various embodiments, the method may further comprise providing the therapeutic. In certain embodiments, the therapeutic is BCNU or CCNU, a functional equivalent, analog, derivative or salt of BCNU or CCNU, or a combination thereof. In some embodiments, the therapeutic is not TMZ or a functional equivalent, analog, derivative or salt of TMZ.

In various embodiments, the present invention provides a method for treating MES cancer subtype in a subject. The method comprises ordering a diagnostic test to determine if the subject has MES cancer subtype; and administering a therapeutically effective amount of the therapeutic to the subject who has been diagnosed with the MES cancer subtype, thereby treating the MES cancer subtype in the subject. In some embodiments, the diagnostic test is performed via methods as described in the present invention. In various embodiments, the method may further comprise providing the therapeutic. In certain embodiments, the therapeutic is TMZ, a functional equivalent, analog, derivative or salt of TMZ, or a combination thereof.

In various embodiments, the cancer is a brain tumor, glioma, high grade glioma (HGG), glioblastoma, or glioblastoma multiforme (GBM). In various embodiments, the subject is a human. In various embodiments, the subject is a mammalian subject including but not limited to human, monkey, ape, dog, cat, cow, horse, goat, pig, rabbit, mouse and rat. In various embodiments, the biological sample comprises a cell, neuron, glia, brain cell, spinal cord cell, brain neuron, brain glia, spinal cord neuron, or spinal cord glia, or a combination thereof. In some embodiments, the biological sample comprises a tumor cell or tissue. In some embodiments, the biological sample comprises a tumor biopsy or sample.

In various embodiments, the therapeutic is a nucleic acid, DNA, RNA, peptide, protein, antibody, aptamer, or small molecule, or a combination thereof. In some embodiments, the therapeutic is an alkylating agent, or a PI3K/AKT/mTOR inhibitor, or a combination thereof. In certain embodiments, the therapeutic is BCNU or CCNU, a functional equivalent, analog, derivative or salt of BCNU or CCNU, or a combination thereof. In certain embodiments, the therapeutic is TMZ, a functional equivalent, analog, derivative or salt of TMZ, or a combination thereof.

Typical dosages of an effective amount of the therapeutic can be in the ranges recommended by the manufacturer where known therapeutic molecules or compounds are used, and also as indicated to the skilled artisan by the in vitro responses in cells or in vivo responses in animal models. Such dosages typically can be reduced by up to about an order of magnitude in concentration or amount without losing relevant biological activity. The actual dosage can depend upon the judgment of the physician, the condition of the patient, and the effectiveness of the therapeutic method based, for example, on the in vitro responsiveness of relevant cultured cells or histocultured tissue sample, or the responses observed in the appropriate animal models. In various embodiments, the therapeutic may be administered once a day (SID/QD), twice a day (BID), three times a day (TID), four times a day (QID), or more, so as to administer an effective amount of the therapeutic to the subject, where the effective amount is any one or more of the doses described herein.

In various embodiments, the therapeutic is administered at about 0.001-0.01, 0.01-0.1, 0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 mg/m², or a combination thereof. In various embodiments, the therapeutic is administered at about 0.001-0.01, 0.01-0.1, 0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 mg/kg, or a combination thereof. In various embodiments, the therapeutic is administered once, twice, three or more times. In various embodiments, the therapeutic is administered about 1-3 times per day, 1-7 times per week, 1-9 times per month, or 1-12 times per year. In various embodiments, the therapeutic is administered for about 1-10 days, 10-20 days, 20-30 days, 30-40 days, 40-50 days, 50-60 days, 60-70 days, 70-80 days, 80-90 days, 90-100 days, 1-6 months, 6-12 months, or 1-5 years. Here, “mg/kg” refers to mg per kg body weight of the subject, and “mg/m2” refers to mg per m2 body surface area of the subject. In certain embodiments, the therapeutic is administered to a human. In certain embodiments, the therapeutic is BCNU or CCNU, a functional equivalent, analog, derivative or salt of BCNU or CCNU, or a combination thereof. In certain embodiments, the therapeutic is TMZ, a functional equivalent, analog, derivative or salt of TMZ, or a combination thereof.

In various embodiments, the effective amount of the therapeutic is any one or more of about 0.001-0.01, 0.01-0.1, 0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 μg/kg/day, or a combination thereof. In various embodiments, the effective amount of the therapeutic is any one or more of about 0.001-0.01, 0.01-0.1, 0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 μg/m²/day, or a combination thereof. In various embodiments, the effective amount of the therapeutic is any one or more of about 0.001-0.01, 0.01-0.1, 0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 mg/kg/day, or a combination thereof. In various embodiments, the effective amount of the therapeutic is any one or more of about 0.001-0.01, 0.01-0.1, 0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 mg/m²/day, or a combination thereof. Here, “m/kg/day” or “mg/kg/day” refers to μg or mg per kg body weight of the subject per day, and “m/m2/day” or “mg/m2/day” refers to μg or mg per m2 body surface area of the subject per day.

In some embodiments, the therapeutic may be administered at the prevention stage of a condition (i.e., when the subject has not developed the condition but is likely to or in the process to develop the condition). In other embodiments, the therapeutic may be administered at the treatment stage of a condition (i.e., when the subject has already developed the condition). As a non-limiting example, the target condition is GBM. In this exemplar situation, the patient may be treated with the methods described herein when the patient has not yet developed GBM, or is likely to develop GBM, or is in the process of developing GBM, or has already developed GBM.

In accordance with the invention, the therapeutic may be administered using the appropriate modes of administration, for instance, the modes of administration recommended by the manufacturer for each of the therapeutic. In accordance with the invention, various routes may be utilized to administer the therapeutic of the claimed methods, including but not limited to aerosol, nasal, oral, transmucosal, transdermal, parenteral, enteral, topical, local, implantable pump, continuous infusion, capsules and/or injections. In various embodiments, the therapeutic is administered intracranially, intraventricularly, intrathecally, epidurally, intradurally, topically, intravascularly, intravenously, intraarterially, intratumorally, intramuscularly, subcutaneously, intraperitoneally, intranasally, or orally.

In various embodiments, the therapeutic is provided as a pharmaceutical composition. In various embodiments, the composition is formulated for via any route of administration, including but not limited to intracranial, intraventricular, intrathecal, epidural, intradural, topical, intravascular, intravenous, intraarterial, intratumoral, intramuscular, subcutaneous, intraperitoneal, intranasal or oral administration. Methods for these administrations are known to one skilled in the art. Preferred pharmaceutical compositions will also exhibit minimal toxicity when administered to a mammal.

In various embodiments, the pharmaceutical compositions according to the invention can contain any pharmaceutically acceptable excipient. “Pharmaceutically acceptable excipient” means an excipient that is useful in preparing a pharmaceutical composition that is generally safe, non-toxic, and desirable, and includes excipients that are acceptable for veterinary use as well as for human pharmaceutical use. Such excipients may be solid, liquid, semisolid, or, in the case of an aerosol composition, gaseous. Examples of excipients include but are not limited to starches, sugars, microcrystalline cellulose, diluents, granulating agents, lubricants, binders, disintegrating agents, wetting agents, emulsifiers, coloring agents, release agents, coating agents, sweetening agents, flavoring agents, perfuming agents, preservatives, antioxidants, plasticizers, gelling agents, thickeners, hardeners, setting agents, suspending agents, surfactants, humectants, carriers, stabilizers, and combinations thereof.

In various embodiments, the pharmaceutical compositions according to the invention can contain any pharmaceutically acceptable carrier. “Pharmaceutically acceptable carrier” as used herein refers to a pharmaceutically acceptable material, composition, or vehicle that is involved in carrying or transporting a compound of interest from one tissue, organ, or portion of the body to another tissue, organ, or portion of the body. For example, the carrier may be a liquid or solid filler, diluent, excipient, solvent, or encapsulating material, or a combination thereof. Each component of the carrier must be “pharmaceutically acceptable” in that it must be compatible with the other ingredients of the formulation. It must also be suitable for use in contact with any tissues or organs with which it may come in contact, meaning that it must not carry a risk of toxicity, irritation, allergic response, immunogenicity, or any other complication that excessively outweighs its therapeutic benefits.

The pharmaceutical compositions according to the invention can also be encapsulated, tableted or prepared in an emulsion or syrup for oral administration. Pharmaceutically acceptable solid or liquid carriers may be added to enhance or stabilize the composition, or to facilitate preparation of the composition. Liquid carriers include syrup, peanut oil, olive oil, glycerin, saline, alcohols and water. Solid carriers include starch, lactose, calcium sulfate, dihydrate, terra alba, magnesium stearate or stearic acid, talc, pectin, acacia, agar or gelatin. The carrier may also include a sustained release material such as glyceryl monostearate or glyceryl distearate, alone or with a wax.

The pharmaceutical preparations are made following the conventional techniques of pharmacy involving dry milling, mixing, and blending for powder forms; milling, mixing, granulation, and compressing, when necessary, for tablet forms; or milling, mixing and filling for hard gelatin capsule forms. When a liquid carrier is used, the preparation will be in the form of a syrup, elixir, emulsion or an aqueous or non-aqueous suspension. Such a liquid formulation may be administered directly p.o. or filled into a soft gelatin capsule.

The pharmaceutical compositions according to the invention may be delivered in a therapeutically effective amount. The precise therapeutically effective amount is that amount of the composition that will yield the most effective results in terms of efficacy of treatment in a given subject. This amount will vary depending upon a variety of factors, including but not limited to the characteristics of the therapeutic compound (including activity, pharmacokinetics, pharmacodynamics, and bioavailability), the physiological condition of the subject (including age, sex, disease type and stage, general physical condition, responsiveness to a given dosage, and type of medication), the nature of the pharmaceutically acceptable carrier or carriers in the formulation, and the route of administration. One skilled in the clinical and pharmacological arts will be able to determine a therapeutically effective amount through routine experimentation, for instance, by monitoring a subject's response to administration of a compound and adjusting the dosage accordingly. For additional guidance, see Remington: The Science and Practice of Pharmacy (Gennaro ed. 20th edition, Williams & Wilkins PA, USA) (2000).

Before administration to patients, formulants may be added to the composition. A liquid formulation may be preferred. For example, these formulants may include oils, polymers, vitamins, carbohydrates, amino acids, salts, buffers, albumin, surfactants, bulking agents or combinations thereof.

Carbohydrate formulants include sugar or sugar alcohols such as monosaccharides, disaccharides, or polysaccharides, or water soluble glucans. The saccharides or glucans can include fructose, dextrose, lactose, glucose, mannose, sorbose, xylose, maltose, sucrose, dextran, pullulan, dextrin, alpha and beta cyclodextrin, soluble starch, hydroxethyl starch and carboxymethylcellulose, or mixtures thereof “Sugar alcohol” is defined as a C4 to C8 hydrocarbon having an —OH group and includes galactitol, inositol, mannitol, xylitol, sorbitol, glycerol, and arabitol. These sugars or sugar alcohols mentioned above may be used individually or in combination. There is no fixed limit to amount used as long as the sugar or sugar alcohol is soluble in the aqueous preparation. In one embodiment, the sugar or sugar alcohol concentration is between 1.0 w/v % and 7.0 w/v %, more preferable between 2.0 and 6.0 w/v %.

Amino acids formulants include levorotary (L) forms of carnitine, arginine, and betaine; however, other amino acids may be added.

Polymers formulants include polyvinylpyrrolidone (PVP) with an average molecular weight between 2,000 and 3,000, or polyethylene glycol (PEG) with an average molecular weight between 3,000 and 5,000.

It is also preferred to use a buffer in the composition to minimize pH changes in the solution before lyophilization or after reconstitution. Most any physiological buffer may be used including but not limited to citrate, phosphate, succinate, and glutamate buffers or mixtures thereof. In some embodiments, the concentration is from 0.01 to 0.3 molar. Surfactants that can be added to the formulation are shown in EP Nos. 270,799 and 268,110.

Another drug delivery system for increasing circulatory half-life is the liposome. Methods of preparing liposome delivery systems are discussed in Gabizon et al., Cancer Research (1982) 42:4734; Cafiso, Biochem Biophys Acta (1981) 649:129; and Szoka, Ann Rev Biophys Eng (1980) 9:467. Other drug delivery systems are known in the art and are described in, e.g., Poznansky et al., DRUG DELIVERY SYSTEMS (R. L. Juliano, ed., Oxford, N.Y. 1980), pp. 253-315; M. L. Poznansky, Pharm Revs (1984) 36:277.

After the liquid pharmaceutical composition is prepared, it may be lyophilized to prevent degradation and to preserve sterility. Methods for lyophilizing liquid compositions are known to those of ordinary skill in the art. Just prior to use, the composition may be reconstituted with a sterile diluent (Ringer's solution, distilled water, or sterile saline, for example) which may include additional ingredients. Upon reconstitution, the composition is administered to subjects using those methods that are known to those skilled in the art.

The compositions of the invention may be sterilized by conventional, well-known sterilization techniques. The resulting solutions may be packaged for use or filtered under aseptic conditions and lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration. The compositions may contain pharmaceutically-acceptable auxiliary substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, and stabilizers (e.g., 1-20% maltose, etc.).

The pharmaceutical composition according to the invention can also be a bead system for delivering the therapeutic agent to the target cells. For example, pectin/zein hydrogel bead system may be used to deliver Neuregulin-4 or a pharmaceutical equivalent, analog, derivative or a salt thereof, to the target cells in the subject (Yan F. et al., J Clin Invest. 2011 June; 121(6):2242-53).

Kits of the Invention

The present invention is also directed to a kit that is used to classify, diagnose and/or treat cancers. The kit is an assemblage of materials or components, including at least one of the inventive elements or modules. Thus, in some embodiments the kit contains one or more detection agents that specifically bind to one or more AKT pathway components, as described above; and in other embodiments the kit contains a cancer therapeutic, as described above. In certain embodiments the kit contains a composition including a drug delivery molecule complexed with a cancer therapeutic, as described above.

In various embodiments, the present invention provides a kit for categorizing/classifying/stratifying a cancer in a subject. The kit may consist of or may consist essentially of or may comprise: one or more detection agents that specifically bind to one or more AKT pathway components; instructions for using the one or more detection agents to classify the cancer in the subject.

In various embodiments, the present invention provides a kit for diagnosing whether a subject has a cancer subtype. The kit may consist of or may consist essentially of or may comprise: one or more detection agents that specifically bind to one or more AKT pathway components; instructions for using the one or more detection agents to diagnose whether a subject has the cancer subtype.

In various embodiments, the present invention provides a kit for treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of a cancer subtype in a subject. The kit may consist of or may consist essentially of or may comprise: one or more detection agents that specifically bind to one or more AKT pathway components; a quantity of a therapeutic; and instructions for using the one or more detection agents and the therapeutic to treat, prevent, reduce the likelihood of having, reduce the severity of and/or slow the progression of the cancer subtype in the subject

In various embodiments, the present invention provides a kit for treating an AKT cancer subtype in a subject. The kit may consist of or may consist essentially of or may comprise: a quantity of a therapeutic; and instructions for using the therapeutic to treat the AKT cancer subtype in the subject.

In various embodiments, the subject is a human. In various embodiments, the cancer is a brain tumor, glioma, high grade glioma (HGG), glioblastoma, or glioblastoma multiforme (GBM). In various embodiments, the cancer subtype is C1, PN, MES, CLAS, SL, or PROLIF subtype.

In various embodiments, the one or more detection agents are applied to contact a biological sample obtained from the subject; and the level of binding between the one or more detection agents and the one or more AKT pathway components is detected to determine expression patterns of AKT pathway components. In some embodiments, the one or more detection agents are oligonucleotide probes, nucleic acids, DNAs, RNAs, peptides, proteins, antibodies, aptamers, or small molecules, or a combination thereof. In various embodiments, the level of binding is detected using a microarray. In some embodiments, the microarray is an oligonucleotide microarray, DNA microarray, cDNA microarrays, RNA microarray, peptide microarray, protein microarray, or antibody microarray, or a combination thereof.

In various embodiments, the therapeutic is a nucleic acid, DNA, RNA, peptide, protein, antibody, aptamer, or small molecule, or a combination thereof. In some embodiments, the therapeutic is an alkylating agent, or a PI3K/AKT/mTOR inhibitor, or a combination thereof. In certain embodiments, the therapeutic is BCNU or CCNU, a functional equivalent, analog, derivative or salt of BCNU or CCNU, or a combination thereof. In certain embodiments, the therapeutic is TMZ, a functional equivalent, analog, derivative or salt of TMZ, or a combination thereof.

The exact nature of the components configured in the inventive kit depends on its intended purpose. In one embodiment, the kit is configured particularly for the purpose of treating mammalian subjects. In another embodiment, the kit is configured particularly for the purpose of treating human subjects. In further embodiments, the kit is configured for veterinary applications, treating subjects such as, but not limited to, farm animals, domestic animals, and laboratory animals.

Instructions for use may be included in the kit. “Instructions for use” typically include a tangible expression describing the technique to be employed in using the components of the kit to affect a desired outcome. Optionally, the kit also contains other useful components, such as, spray bottles or cans, diluents, buffers, pharmaceutically acceptable carriers, syringes, catheters, applicators (for example, applicators of cream, gel or lotion etc.), pipetting or measuring tools, bandaging materials or other useful paraphernalia as will be readily recognized by those of skill in the art.

The materials or components assembled in the kit can be provided to the practitioner stored in any convenient and suitable ways that preserve their operability and utility. For example the detection agents and/or cancer therapeutics can be in dissolved, dehydrated, or lyophilized form; they can be provided at room, refrigerated or frozen temperatures. The components are typically contained in suitable packaging material(s). As employed herein, the phrase “packaging material” refers to one or more physical structures used to house the contents of the kit, such as inventive compositions and the like. The packaging material is constructed by well-known methods, preferably to provide a sterile, contaminant-free environment. The packaging materials employed in the kit are those customarily utilized in assays and therapies. As used herein, the term “package” refers to a suitable solid matrix or material such as glass, plastic, paper, foil, and the like, capable of holding the individual kit components. Thus, for example, a package can be a glass vial used to contain suitable quantities of a composition as described herein. The packaging material generally has an external label which indicates the contents and/or purpose of the kit and/or its components.

Compositions

The present invention is also directed to a composition that is used to classify and/or diagnose cancers and cancer subtypes.

In some embodiments, the composition comprises one or more detection agents that specifically bind to one or more AKT pathway components, as described herein; and a biological sample from a subject desiring a classification or diagnosis regarding a cancer.

In various embodiments, the composition comprises one or more detection agents that specifically bind to one or more AKT pathway components; as described herein; and a biological sample from a subject desiring a classification regarding a cancer.

In various embodiments, the composition one or more detection agents that specifically bind to one or more AKT pathway components; and a biological sample from a subject desiring a subject diagnosis on whether he/she has the cancer subtype.

In various embodiments, the cancer subtype is C1, PN, MES, CLAS, SL, or PROLIF subtype.

Systems and Computers

In certain embodiments, the methods of the invention implement a computer program to calculate a copy number, copy number loss, copy number gain, LOH, mutation, deletion and expression levels. For example, a computer program can be used to perform the algorithms described herein. A computer system can also store and manipulate data generated by the methods of the present invention which comprises a plurality of hybridization signal changes/profiles during approach to equilibrium in different hybridization measurements and which can be used by a computer system in implementing the methods of this invention. In certain embodiments, a computer system receives probe hybridization data; (ii) stores probe hybridization data; and (iii) compares probe hybridization data to determine the state of AKT pathway components and genomic loci in a biological sample from cancerous or pre-cancerous tissue. The copy number, copy number loss, copy number gain, LOH, mutation, deletion and expression levels is then calculated. In some embodiments, a computer system (i) compares the determined copy number, copy number loss, copy number gain, LOH, mutation, deletion and expression levels to a threshold value or reference value; and (ii) outputs an indication of whether said copy number, copy number loss, copy number gain, LOH, mutation, deletion and expression levels is above or below a threshold value, or a genetic signature based on said indication. In certain embodiments, such computer systems are also considered part of the present invention.

Numerous types of computer systems can be used to implement the analytic methods of this invention according to knowledge possessed by a skilled artisan in the bioinformatics and/or computer arts.

Several software components can be loaded into memory during operation of such a computer system. The software components can comprise both software components that are standard in the art and components that are special to the present invention (e.g., dCHIP software described in Lin et al. (2004) Bioinformatics 20, 1233-1240; CRLMM software described in Silver et al. (2007) Cell 128, 991-1002; Aroma Affymetrix software described in Richardson et al. (2006) Cancer Cell 9, 121-132. The methods of the invention can also be programmed or modeled in mathematical software packages that allow symbolic entry of equations and high-level specification of processing, including specific algorithms to be used, thereby freeing a user of the need to procedurally program individual equations and algorithms. Such packages include, e.g., Matlab from Mathworks (Natick, Mass.), Mathematica from Wolfram Research (Champaign, Ill.) or S-Plus from MathSoft (Seattle, Wash.). In certain embodiments, the computer comprises a database for storage of hybridization signal profiles. Such stored profiles can be accessed and used to calculate a copy number, copy number loss, copy number gain, LOH, mutation, deletion and expression level. For example, of the hybridization signal profile of a sample derived from the non-cancerous tissue of a subject and/or profiles generated from population-based distributions of AKT pathway components and genomic loci in relevant populations of the same species were stored, it could then be compared to the hybridization signal profile of a sample derived from the cancerous tissue of the subject.

In addition to the exemplary program structures and computer systems described herein, other, alternative program structures and computer systems will be readily apparent to the skilled artisan. Such alternative systems, which do not depart from the above described computer system and programs structures either in spirit or in scope, are therefore intended to be comprehended within the accompanying claims.

Once a laboratory technician or laboratory professional or group of laboratory technicians or laboratory professionals determines whether a sample has a copy number, copy number gain, copy number loss, or expression level as described above (e.g., step (1) in many of the methods above), the same or a different laboratory technician or laboratory professional (or group) can analyze a plurality of tests of AKT pathway components and genomic loci to determine whether there is a copy number, copy number loss, copy number gain, LOH, mutation, or deletion to determine the expression levels (e.g., step (2) in many of the methods above). Next, the same or a different laboratory technician or laboratory professional (or group) can combine copy number, copy number loss, copy number gain, LOH, mutation, or deletion, or expression level data from the test of AKT pathway components and genomic loci to derive a copy number, copy number loss, copy number gain, LOH, mutation, or deletion, or expression level (e.g., step (3) in many of the methods above). Optionally, the same or a different laboratory technician or laboratory professional (or group) can correlate the copy number, copy number loss, LOH, mutation, or deletion, or expression level to an increased or decreased likelihood of response to a particular therapy (e.g., those mentioned above).

In various embodiments, provided herein is a computer readable storage medium comprising: a storing data module containing data from a sample comprising a cancer cell obtained from a subject that represents an expression level from an assay for AKT pathway components and genomic loci; a comparison module that compares the data stored on the storing data module with a reference data and/or control data, and to provide a comparison content, and an output module displaying the comparison content for the user, wherein the expression pattern of AKT pathway components and genomic loci indicates that the subject is has a certain AKT cancer subtype and an appropriate therapy that is likely effective to this AKT cancer subtype should be selected or prescribed and administered to the subject as the subject may not adequately respond to other therapies. Also, the subject may be instructed to take the appropriate therapy that is likely effective to his or her AKT cancer subtype.

In various embodiments, the control data comprises data from a population of cancer patients. In various embodiments, the control data comprises data from a population of non-cancerous healthy individuals. In various embodiments, the control data comprises data from a housekeeping gene expression.

Embodiments of the invention can be described through functional modules, which are defined by computer executable instructions recorded on computer readable media and which cause a computer to perform method steps when executed. The modules are segregated by function, for the sake of clarity. However, it should be understood that the modules/systems need not correspond to discreet blocks of code and the described functions can be carried out by the execution of various code portions stored on various media and executed at various times. Furthermore, it should be appreciated that the modules may perform other functions, thus the modules are not limited to having any particular functions or set of functions.

The computer readable storage media can be any available tangible media that can be accessed by a computer. Computer readable storage media includes volatile and nonvolatile, removable and non-removable tangible media implemented in any method or technology for storage of information such as computer readable instructions, data structures, program modules or other data. Computer readable storage media includes, but is not limited to, RAM (random access memory), ROM (read only memory), EPROM (erasable programmable read only memory), EEPROM (electrically erasable programmable read only memory), flash memory or other memory technology, CD-ROM (compact disc read only memory), DVDs (digital versatile disks), BLU-RAY disc or other optical storage media, magnetic cassettes, magnetic tape, magnetic disk storage or other magnetic storage media, other types of volatile and non-volatile memory, and any other tangible medium which can be used to store the desired information and which can accessed by a computer including and any suitable combination of the foregoing.

Computer-readable data embodied on one or more computer-readable media may define instructions, for example, as part of one or more programs that, as a result of being executed by a computer, instruct the computer to perform one or more of the functions described herein, and/or various embodiments, variations and combinations thereof. Such instructions may be written in any of a plurality of programming languages, for example, Java, J#, Visual Basic, C, C#, C++, Fortran, Pascal, Eiffel, Basic, COBOL assembly language, and the like, or any of a variety of combinations thereof. The computer-readable media on which such instructions are embodied may reside on one or more of the components of either of a system, or a computer readable storage medium described herein, may be distributed across one or more of such components.

The computer-readable media may be transportable such that the instructions stored thereon can be loaded onto any computer resource to implement the aspects of the present invention discussed herein. In addition, it should be appreciated that the instructions stored on the computer-readable medium, described above, are not limited to instructions embodied as part of an application program running on a host computer. Rather, the instructions may be embodied as any type of computer code (e.g., software or microcode) that can be employed to program a computer to implement aspects of the present invention. The computer executable instructions may be written in a suitable computer language or combination of several languages. Basic computational biology methods are known to those of ordinary skill in the art and are described in, for example, Setubal and Meidanis et al., Introduction to Computational Biology Methods (PWS Publishing Company, Boston, 1997); Salzberg, Searles, Kasif, (Ed.), Computational Methods in Molecular Biology, (Elsevier, Amsterdam, 1998); Rashidi and Buehler, Bioinformatics Basics: Application in Biological Science and Medicine (CRC Press, London, 2000) and Ouelette and Bzevanis Bioinformatics: A Practical Guide for Analysis of Gene and Proteins (Wiley & Sons, Inc., 2nd ed., 2001).

The functional modules of certain embodiments of the invention include for example, at a measuring module, a storage module, a comparison module, and an output module. The functional modules can be executed on one, or multiple, computers, or by using one, or multiple, computer networks. The measuring module has computer executable instructions to provide e.g., expression information in non-transitory computer readable form.

The measuring module can comprise any system for detecting the expression patterns of AKT pathway components and status of genetic loci (e.g., copy number alterations, copy number gain or loss, LOH, mutations, amplifications and deletions). Such systems can include DNA microarrays, RNA expression arrays, any ELISA detection system and/or any Western blotting detection system.

The information determined in the determination system can be read by the storage module. As used herein the “storage module” is intended to include any suitable computing or processing apparatus or other device configured or adapted for storing data or information. Examples of electronic apparatus suitable for use with the present invention include stand-alone computing apparatus, data telecommunications networks, including local area networks (LAN), wide area networks (WAN), Internet, Intranet, and Extranet, and local and distributed computer processing systems. Storage modules also include, but are not limited to: magnetic storage media, such as floppy discs, hard disc storage media, magnetic tape, optical storage media such as CD-ROM, DVD, electronic storage media such as RAM, ROM, EPROM, EEPROM and the like, general hard disks and hybrids of these categories such as magnetic/optical storage media. The storage module is adapted or configured for having recorded thereon expression level or protein level information. Such information may be provided in digital form that can be transmitted and read electronically, e.g., via the Internet, on diskette, via USB (universal serial bus) or via any other suitable mode of communication.

As used herein, “stored” refers to a process for encoding information on the storage module. Those skilled in the art can readily adopt any of the presently known methods for recording information on known media to generate manufactures comprising expression level information.

In one embodiment the reference data stored in the storage module to be read by the comparison module is, for example, expression data obtained from a population of non-cancer subjects, a population of cancer subjects, or expression data obtained from the same subject at a prior time point using the measuring module.

The “comparison module” can use a variety of available software programs and formats for the comparison operative to compare expression data determined in the measuring module to reference samples and/or stored reference data. In one embodiment, the comparison module is configured to use pattern recognition techniques to compare information from one or more entries to one or more reference data patterns. The comparison module may be configured using existing commercially-available or freely-available software for comparing patterns, and may be optimized for particular data comparisons that are conducted. The comparison module provides computer readable information related to the expression patterns of AKT pathway components and status of genetic loci (e.g., copy number alterations, copy number gain or loss, LOH, mutations, amplifications and deletions) in an individual, efficacy of treatment in an individual, and/or method for treating an individual.

The comparison module, or any other module of the invention, may include an operating system (e.g., UNIX) on which runs a relational database management system, a World Wide Web application, and a World Wide Web server. World Wide Web application includes the executable code necessary for generation of database language statements (e.g., Structured Query Language (SQL) statements). Generally, the executables will include embedded SQL statements. In addition, the World Wide Web application may include a configuration file which contains pointers and addresses to the various software entities that comprise the server as well as the various external and internal databases which must be accessed to service user requests. The Configuration file also directs requests for server resources to the appropriate hardware—as may be necessary should the server be distributed over two or more separate computers. In one embodiment, the World Wide Web server supports a TCP/IP protocol. Local networks such as this are sometimes referred to as “Intranets. An advantage of such Intranets is that they allow easy communication with public domain databases residing on the World Wide Web (e.g., the GenBank or Swiss Pro World Wide Web site). Thus, in a particular preferred embodiment of the present invention, users can directly access data (via Hypertext links for example) residing on Internet databases using a HTML interface provided by Web browsers and Web servers.

The comparison module provides a computer readable comparison result that can be processed in computer readable form by predefined criteria, or criteria defined by a user, to provide a content-based in part on the comparison result that may be stored and output as requested by a user using an output module.

The content based on the comparison result, may be an expression value compared to a reference showing the susceptibility/adequate response or nonsusceptibility/non-adequate response from standard, conventional or certain therapy.

In various embodiments of the invention, the content based on the comparison result is displayed on a computer monitor. In various embodiments of the invention, the content based on the comparison result is displayed through printable media. The display module can be any suitable device configured to receive from a computer and display computer readable information to a user. Non-limiting examples include, for example, general-purpose computers such as those based on Intel PENTIUM-type processor, Motorola PowerPC, Sun UltraSPARC, Hewlett-Packard PA-RISC processors, any of a variety of processors available from Advanced Micro Devices (AMD) of Sunnyvale, Calif., or any other type of processor, visual display devices such as flat panel displays, cathode ray tubes and the like, as well as computer printers of various types.

In one embodiment, a World Wide Web browser is used for providing a user interface for display of the content based on the comparison result. It should be understood that other modules of the invention can be adapted to have a web browser interface. Through the Web browser, a user may construct requests for retrieving data from the comparison module. Thus, the user will typically point and click to user interface elements such as buttons, pull down menus, scroll bars and the like conventionally employed in graphical user interfaces.

The present invention therefore provides for systems (and computer readable media for causing computer systems) to perform methods for selecting treatment of cancer in an individual. As used herein, “selecting treatment” refers to selecting, choosing or prescribing a cancer treatment for the individual, or instructing or directing the individual to receive a cancer treatment.

Systems and computer readable media described herein are merely illustrative embodiments of the invention for detecting the expression patterns of AKT pathway components and status of genetic loci (e.g., copy number alterations, copy number gain or loss, LOH, mutations, amplifications and deletions) in an individual, and are not intended to limit the scope of the invention. Variations of the systems and computer readable media described herein are possible and are intended to fall within the scope of the invention.

The modules of the machine, or those used in the computer readable medium, may assume numerous configurations. For example, function may be provided on a single machine or distributed over multiple machines.

In some cases, a computing system provided herein can include computer-executable instructions or a computer program (e.g., software) containing computer-executable instructions for formatting an output providing an indication the expression patterns of AKT pathway components and status of genetic loci (e.g., copy number alterations, copy number gain or loss, LOH, mutations, amplifications and deletions) or a likelihood that a cancer patient will respond to a particular cancer treatment regimen (e.g., a regimen as described above), or a combination of these items. In some cases, a computing system provided herein can include computer-executable instructions or a computer program (e.g., software) containing computer-executable instructions for determining a desired cancer treatment regimen for a particular patient based at least in part on the expression patterns of AKT pathway components and status of genetic loci (e.g., copy number alterations, copy number gain or loss, LOH, mutations, amplifications and deletions).

In some cases, a computing system provided herein can include a pre-processing device configured to process a sample (e.g., cancer cells) such that a SNP array-based assay or sequencing-based assay can be performed. Examples of pre-processing devices include, without limitation, devices configured to enrich cell populations for cancer cells as opposed to non-cancer cells, devices configured to lyse cells and/or extract genomic nucleic acid, and devices configured to enrich a sample for particular genomic DNA fragments.

Expression Pattern Assay—RNA

In various embodiments, determining an expression pattern of AKT pathway components in the biological sample comprises assaying mRNA levels. In various embodiments, assaying mRNA levels comprises using RNA sequencing, northern blot, in situ hybridization, hybridization array, serial analysis of gene expression (SAGE), reverse transcription PCR, real-time PCR, real-time reverse transcription PCR, quantitative PCR, or microarray, or a combination thereof.

In various embodiments, assaying mRNA levels comprises contacting the biological sample with polynucleotide probes capable of specifically hybridizing to mRNA of one or more AKT pathway components and thereby forming probe-target hybridization complexes.

Hybridization-based RNA assays include, but are not limited to, traditional “direct probe” methods such as, northern blot or in situ hybridization (e.g., Angerer (1987) Meth. Enzymol 152: 649). The methods can be used in a wide variety of formats including, but not limited to, substrate (e.g. membrane or glass) bound methods or array-based approaches. In a typical in situ hybridization assay, cells are fixed to a solid support, typically a glass slide. If a nucleic acid is to be probed, the cells are typically denatured with heat or alkali. The cells are then contacted with a hybridization solution at a moderate temperature to permit annealing of labeled probes specific to the nucleic acid sequence encoding the protein. The targets (e.g., cells) are then typically washed at a predetermined stringency or at an increasing stringency until an appropriate signal to noise ratio is obtained. The probes are typically labeled, e.g., with radioisotopes or fluorescent reporters. Preferred probes are sufficiently long so as to specifically hybridize with the target nucleic acid(s) under stringent conditions. The preferred size range is from about 200 bases to about 1000 bases. Hybridization protocols suitable for use with the methods of the invention are described, e.g., in Albertson (1984) EMBO J. 3: 1227-1234; Pinkel (1988) Proc. Natl. Acad. Sci. USA 85: 9138-9142; EPO Pub. No. 430,402; Methods in Molecular Biology, Vol. 33: In situ Hybridization Protocols, Choo, ed., Humana Press, Totowa, N.J. (1994), Pinkel, et al. (1998) Nature Genetics 20: 207-211, and/or Kallioniemi (1992) Proc. Natl Acad Sci USA 89:5321-5325 (1992). In some applications, it is necessary to block the hybridization capacity of repetitive sequences. Thus, in some embodiments, tRNA, human genomic DNA, or Cot-I DNA is used to block non-specific hybridization.

In various embodiments, assaying mRNA levels comprises contacting the biological sample with polynucleotide primers capable of specifically hybridizing to mRNAs of genes listed in Table 2, Table 4, Table 5, or Table 6, forming primer-template hybridization complexes, and performing a PCR reaction. In some embodiments, the polynucleotide primers comprises about 15-45, 20-40, or 25-35 bp sequences that are identical (for forward primers) or complementary (for reverse primers) to sequences of genes listed in Table 2, Table 4, Table 5, or Table 6. As a non-liming example, the polynucleotide primers for ACLY (e.g., transcript variant 1 NM_001096.2 with 4450 bp) can comprise sequences that are identical (for forward primers) or complementary (for reverse primers) to ACLY's bp 1-20, 5-25, 10-30, 15-35, 20-40, 25-45, 30-50, so on and so forth, until the end of ACLY, 4410-4430, 4415-4435, 4420-4440, 4425-4445, 4430-4450. While not listed here exhaustively because of the space, all these polynucleotide primers for ACLY and other genes listed in Table 2, Table 4, Table 5, or Table 6 can be used in the present invention. In various embodiments, the polynucleotide primers are labeled with radioisotopes or fluorescent molecules. As the labeled primers emit radio or fluorescent signals, the PCR products containing the labeled primers can be detected and analyzed with a variety of imaging equipment.

Methods of “quantitative” amplification are well known to those of skill in the art. For example, quantitative PCR involves simultaneously co-amplifying a known quantity of a control sequence using the same primers. This provides an internal standard that may be used to calibrate the PCR reaction. Detailed protocols for quantitative PCR are provided in Innis, et al. (1990) PCR Protocols, A Guide to Methods and Applications, Academic Press, Inc. N.Y.). Measurement of DNA copy number at microsatellite loci using quantitative PCR anlaysis is described in Ginzonger, et al. (2000) Cancer Research 60:5405-5409. The known nucleic acid sequence for the genes is sufficient to enable one of skill in the art to routinely select primers to amplify any portion of the gene. Fluorogenic quantitative PCR may also be used in the methods of the invention. In fluorogenic quantitative PCR, quantitation is based on amount of fluorescence signals, e.g., TaqMan and sybr green. Other suitable amplification methods include, but are not limited to, ligase chain reaction (LCR) (see Wu and Wallace (1989) Genomics 4: 560, Landegren, et al. (1988) Science 241:1077, and Barringer et al. (1990) Gene 89: 117), transcription amplification (Kwoh, et al. (1989) Proc. Natl. Acad. Sci. USA 86: 1173), self-sustained sequence replication (Guatelli, et al. (1990) Proc. Nat. Acad. Sci. USA 87: 1874), dot PCR, and linker adapter PCR, etc.

Expression Level Assay—Protein

In various embodiments, determining an expression pattern of AKT pathway components in the biological sample comprises assaying protein levels. In various embodiments, assaying a protein level comprises using western blot, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay, or mass spectrometry, or a combination thereof.

In various embodiments, assaying protein levels comprises contacting the biological sample with antibodies capable of specifically binding to proteins encoded by genes listed in Table 2, Table 4, Table 5, or Table 6 and thereby forming antigen-antibody complexes. In the methods and assays of the invention, the expression levels of proteins encoded by genes listed in Table 2, Table 4, Table 5, or Table 6, or fragments or variants thereof can be determined using antibodies specific for those individual proteins or fragments or variants thereof and detecting immunospecific binding of each antibody to its respective cognate biomarker protein.

Antibodies, both polyclonal and monoclonal, can be produced by a skilled artisan either by themselves using well known methods or they can be manufactured by service providers who specialize making antibodies based on known protein sequences. In the present invention, the protein sequences of AKT pathway genes are known and thus production of antibodies against them is a matter of routine.

For example, production of monoclonal antibodies can be performed using the traditional hybridoma method by first immunizing mice with an antigen which may be an isolated protein of choice or fragment thereof (for example, a protein encode by a gene listed in Table 2, Table 4, Table 5, or Table 6, or a fragment thereof or a variant thereof) and making hybridoma cell lines that each produce a specific monoclonal antibody. The antibodies secreted by the different clones are then assayed for their ability to bind to the antigen using, e.g., ELISA or Antigen Microarray Assay, or immuno-dot blot techniques. The antibodies that are most specific for the detection of the protein of interest can be selected using routine methods and using the antigen used for immunization and other antigens as controls. The antibody that most specifically detects the desired antigen and protein and no other antigens or proteins are selected for the processes, assays and methods described herein. The best clones can then be grown indefinitely in a suitable cell culture medium. They can also be injected into mice (in the peritoneal cavity, surrounding the gut) where they produce an antibody-rich ascites fluid from which the antibodies can be isolated and purified. The antibodies can be purified using techniques that are well known to one of ordinary skill in the art.

Any suitable immunoassay method may be utilized, including those which are commercially available, to determine the expression level of an AKT pathway protein or a variant thereof assayed according to the invention. Extensive discussion of the known immunoassay techniques is not required here since these are known to those of skill in the art. Typical suitable immunoassay techniques include sandwich enzyme-linked immunoassays (ELISA), radioimmunoassays (MA), competitive binding assays, homogeneous assays, heterogeneous assays, etc.

For example, in the assays of the invention, “sandwich-type” assay formats can be used. An alternative technique is the “competitive-type” assay. In a competitive assay, the labeled probe is generally conjugated with a molecule that is identical to, or an analog of, the analyte. Thus, the labeled probe competes with the analyte of interest for the available receptive material. Competitive assays are typically used for detection of analytes such as haptens, each hapten being monovalent and capable of binding only one antibody molecule.

The antibodies can be labeled. In some embodiments, the detection antibody is labeled by covalently linking to an enzyme, label with a fluorescent compound or metal, label with a chemiluminescent compound. For example, the detection antibody can be labeled with catalase and the conversion uses a colorimetric substrate composition comprises potassium iodide, hydrogen peroxide and sodium thiosulphate; the enzyme can be alcohol dehydrogenase and the conversion uses a colorimetric substrate composition comprises an alcohol, a pH indicator and a pH buffer, wherein the pH indicator is neutral red and the pH buffer is glycine-sodium hydroxide; the enzyme can also be hypoxanthine oxidase and the conversion uses a colorimetric substrate composition comprises xanthine, a tetrazolium salt and 4,5-dihydroxy-1,3-benzene disulphonic acid. In one embodiment, the detection antibody is labeled by covalently linking to an enzyme, label with a fluorescent compound or metal, or label with a chemiluminescent compound.

Direct and indirect labels can be used in immunoassays. A direct label can be defined as an entity, which in its natural state, is visible either to the naked eye or with the aid of an optical filter and/or applied stimulation, e.g., ultraviolet light, to promote fluorescence. Examples of colored labels which can be used include metallic sol particles, gold sol particles, dye sol particles, dyed latex particles or dyes encapsulated in liposomes. Other direct labels include radionuclides and fluorescent or luminescent moieties. Indirect labels such as enzymes can also be used according to the invention. Various enzymes are known for use as labels such as, for example, alkaline phosphatase, horseradish peroxidase, lysozyme, glucose-6-phosphate dehydrogenase, lactate dehydrogenase and urease.

The antibody can be attached to a surface. Examples of useful surfaces on which the antibody can be attached for the purposes of detecting the desired antigen include nitrocellulose, PVDF, polystyrene, and nylon.

In some embodiments of the processes, assays and methods described herein, detecting the level of antibodies reactive to an AKT pathway protein or a variant thereof includes contacting the sample from the cancer patient with an antibody or a fragment thereof that specifically binds an AKT pathway protein or a variant thereof, forming an antibody-protein complex between the antibody and the AKT pathway protein or the variant thereof present in the sample, washing the sample to remove the unbound antibody, adding a detection antibody that is labeled and is reactive to the antibody bound to the AKT pathway protein or a variant thereof in the sample, washing to remove the unbound labeled detection antibody and converting the label to a detectable signal, wherein the detectable signal is indicative of the level of AKT pathway protein or a variant thereof in the sample from the patient. In some embodiments, the effector component is a detectable moiety selected from the group consisting of a fluorescent label, a radioactive compound, an enzyme, a substrate, an epitope tag, electron-dense reagent, biotin, digonigenin, hapten and a combination thereof. In some embodiments, the detection antibody is labeled by covalently linking to an enzyme, labeled with a fluorescent compound or metal, labeled with a chemiluminescent compound. The level of AKT pathway protein may be obtained by assaying a light scattering intensity resulting from the formation of an antibody-protein complex formed by a reaction of AKT pathway protein in the sample with the antibody, wherein the light scattering intensity of at least 10% above a control light scattering intensity indicates the likelihood of chemotherapy resistance.

Reference Value of Expression Level

Various methods described herein may compare an AKT pathway gene's expression level in a subject's biological sample to a pre-determined reference value of the AKT pathway gene. In various embodiments, an AKT pathway gene's reference value of expression level is the AKT pathway gene's median or mean expression level from all tumor samples in the discovery dataset. In various embodiments, an AKT pathway gene's reference value of expression level is the AKT pathway gene's median or mean expression level from all GBM samples in the discovery dataset. In various embodiments, an AKT pathway gene's reference value of expression level is the AKT pathway gene's median or mean expression level from all tumor samples in the validation dataset. In various embodiments, an AKT pathway gene's reference value of expression level is the AKT pathway gene's median or mean expression level from all GBM samples in the validation dataset. In various embodiments, an AKT pathway gene's reference value of expression level is the AKT pathway gene's median or mean expression level from non-cancerous, non-tumorous, or non-neoplastic cells or tissues. In accordance with the present invention, AKT pathway genes include but are not limited to those listed in Table 2, Table 4, Table 5, or Table 6.

Reference values may be obtained by various methods known in the field. For example, one or more biopsies from one cancer patient' tumor (hereinafter “Tumor-1”) may be collected, processed and analyzed to obtain the expression level of one AKT pathway gene (hereinafter “Gene-1”) in this tumor (hereinafter “Expression-Tumor-1-Gene-1”). The same step is used to obtain Gene-1's expression levels in another 10, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000 or more cancer patients' tumors (hereinafter “Tumor-N), that is, “Expression-Tumor-N-Gene-1” (N is 1, 2, 3, 4, 5, 6, 7, . . . ). Then, Gene-1's median or mean expression level from all tumors may be used as the reference value of Gene-1 (hereinafter “REF-Gene-1”), to which Gene-1's expression in a subject's biological sample is compared to so as to determine if Gene-1's expression is high or low in the subject's biological sample. In other words, REF-Gene-1 is the median or mean of Expression-Tumor-N-Gene-1. Similar steps may be used to obtain another 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, or more AKT pathway genes' reference values, that is, “REF-Gene-M” (M=1, 2, 3, 4, 5, 6, 7, . . . ). In various embodiments, non-limiting AKT pathway genes (i.e., Gene-M) are listed in Table 2, Table 4, Table 5, or Table 6. To determine the expression pattern of AKT pathway genes in a subject's biological sample, one may compare one, two, three, four, five, or more AKT pathway genes' expression levels to their respective reference values.

As used herein, “expression pattern”, “expression profile” and “expression signature” are exchangeable terms referring to the specific combination or setting of one or more genes' high (increased) expressions and/or low (decreased) expressions relative to reference values. In various embodiments, AKT cancer subtypes' expression patterns are the specific combinations of AKT pathway genes' high and low expressions. For non-limiting example, FIG. 10 or Table 6 shows the expression patterns of AKT MES, CLAS, PROLIF, SL and SN subtypes in the validation and discovery datasets. Among the 64 exemplar AKT pathway genes shown in FIG. 10 or Table 6, those having high expressions relative to reference values are shown as red, and those having low expressions relative to reference values are shown as green.

Various statistical methods, for example, a two-tailed student t-test with unequal variation, may be used to measure the differences in expression levels of an AKT pathway gene between the subject's sample and a reference value of expression level generate by computer algorithm pooling many tumor samples, as described herein, for example, all the GBM samples in the discovery dataset and/or validation dataset. Various statistical methods, for example, a two-tailed student t-test with unequal variation, may be used to measure the differences in expression levels of an AKT pathway gene between the subject's sample and a control sample from a normal/healthy individual. Various statistical methods, for example, a two-tailed student t-test with unequal variation, may be used to measure the differences in expression levels of an AKT pathway gene between the subject's sample and a reference value of expression level generate by computer algorithm pooling many control samples, as described herein. A significant difference may be achieved where the p value is equal to or less than 0.05.

In various embodiments, the expression level of an AKT pathway gene or a variant thereof in the subject as compared to the reference value is higher by at least or about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100%. In various embodiments, the expression level of an AKT pathway gene or a variant thereof in the subject as compared to the reference value is lower by at least or about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100%. In various embodiments, the expression level ratio between an AKT pathway gene or a variant thereof in the subject and the reference value is at least or about 1.1:1, 1.2:1, 1.3:1, 1.4:1, 1.5:1, 1.6:1, 1.7:1, 1.8:1, 1.9:1, 2:1, 2.1:1, 2.2:1, 2.3:1, 2.4:1, 2.5:1, 2.6:1, 2.7:1, 2.8:1, 2.9:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1 or 10:1, 15:1, 20:1, 25:1, 30:1, 35:1, 40:1, 45:1, 50:1, 55:1, 60:1, 65:1, 70:1, 75:1, 80:1, 85:1, 90:1, 95:1, or 100:1. In various embodiments, the expression level ratio between the reference value and an AKT pathway gene or a variant thereof in the subject is at least or about 1.1:1, 1.2:1, 1.3:1, 1.4:1, 1.5:1, 1.6:1, 1.7:1, 1.8:1, 1.9:1, 2:1, 2.1:1, 2.2:1, 2.3:1, 2.4:1, 2.5:1, 2.6:1, 2.7:1, 2.8:1, 2.9:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1 or 10:1, 15:1, 20:1, 25:1, 30:1, 35:1, 40:1, 45:1, 50:1, 55:1, 60:1, 65:1, 70:1, 75:1, 80:1, 85:1, 90:1, 95:1, or 100:1.

Many variations and alternative elements have been disclosed in embodiments of the present invention. Still further variations and alternate elements will be apparent to one of skill in the art. Among these variations, without limitation, are the selection of constituent modules for the inventive compositions, and the diseases and other clinical conditions that may be diagnosed, prognosed or treated therewith. Various embodiments of the invention can specifically include or exclude any of these variations or elements.

In some embodiments, the numbers expressing quantities of ingredients, properties such as concentration, reaction conditions, and so forth, used to describe and claim certain embodiments of the invention are to be understood as being modified in some instances by the term “about.” Accordingly, in some embodiments, the numerical parameters set forth in the written description and attached claims are approximations that can vary depending upon the desired properties sought to be obtained by a particular embodiment. In some embodiments, the numerical parameters should be construed in light of the number of reported significant digits and by applying ordinary rounding techniques. Notwithstanding that the numerical ranges and parameters setting forth the broad scope of some embodiments of the invention are approximations, the numerical values set forth in the specific examples are reported as precisely as practicable. The numerical values presented in some embodiments of the invention may contain certain errors necessarily resulting from the standard deviation found in their respective testing measurements.

Groupings of alternative elements or embodiments of the invention disclosed herein are not to be construed as limitations. Each group member can be referred to and claimed individually or in any combination with other members of the group or other elements found herein. One or more members of a group can be included in, or deleted from, a group for reasons of convenience and/or patentability. When any such inclusion or deletion occurs, the specification is herein deemed to contain the group as modified thus fulfilling the written description of all Markush groups used in the appended claims.

EXAMPLES

The invention will be further explained by the following Examples, which are intended to be purely exemplary of the invention, and should not be considered as limiting the invention in any way. The following examples are provided to better illustrate the claimed invention and are not to be interpreted as limiting the scope of the invention. To the extent that specific materials are mentioned, it is merely for purposes of illustration and is not intended to limit the invention. One skilled in the art may develop equivalent means or reactants without the exercise of inventive capacity and without departing from the scope of the invention.

Example 1: Materials and Methods

Patient Information

The discovery dataset (GBM195) consisted of 181 GBM (WHO grade IV astrocytoma; (159 primary and 22 recurrent) from 3 datasets [3], [4], [21] and 14 non-neoplastic samples from 2 sources: (1) six samples from patients undergoing temporal lobe epilepsy surgery [3] and (2) eight samples from autopsy specimens of cerebral cortex from donors with no history of neurological disorders obtained from the National Neurological Research Brain Bank (Los Angeles, Calif.) [4]. Two datasets are in GEO (GSE4271, GSE4412) and the third has been submitted. Table 1 lists GEO ID's and clinical information for GBM195 tumors. Tissue collection and processing, pathological review, and microarray analysis for the discovery dataset (GBM195) has been described elsewhere ([3] Nigro et al. 2005, [4] Phillips et a. 2006, and [21] Freije et al. 2004, which are incorporated herein by reference in their entirety as though fully set forth.) The validation dataset consisted of 583 samples; 573 GBM (16 recurrent and 3 secondary) and 10 non-neoplastic samples from The Cancer Genome Atlas (TCGA). Samples were collected and processed as described ([5] Atlas TCG 2008, which is incorporated herein by reference in its entirety as though fully set forth.). IRB or Committee on Human Research approval was obtained for samples used in the discovery and validation datasets as described [3], [4], [10], [21].

TABLE 1 Clinical information for tumors in GBM195 GEO_Accessions Phillips Survival Censoring id (U133A/U133B) Histology Anat. Site Recurrence Subclass Gender Age Weeks Status G1022 GSM99544, GSM99545 GBM Mes male 31 18 D G1028 GSM99465, GSM99464 GBM Unk female 20 7.7 D G1032 GSM99483, GSM99482 GBM PN female 34 12.9 D G1038 GSM99581, GSM99580 GBM PN female 33 178.1 A G1043 GSM99560, GSM99561 GBM Mes female 23 155.6 D G1334 GSM99529, GSM99528 GBM PN female 36 43.1 D G1342 GSM99471, GSM99470 GBM PN male 54 32 D G1354 GSM99551, GSM99550 GBM Mes male 42 60 D G1398 GSM99491, GSM99490 GBM Mes female 49 41.9 D G1406 GSM99543, GSM99542 GBM Mes male 29 33.7 D G1414 GSM99466, GSM99467 GBM Mes female 69 9.1 D G1423 GSM99493, GSM99492 GBM PN female 54 13.7 D G1463 GSM99475, GSM99474 GBM PN male 30 37.9 D G1469 GSM99494, GSM99495 GBM Mes male 56 21.9 D G1478 GSM99553, GSM99552 GBM PN male 40 155.4 A G1495 GSM99457, GSM99456 GBM PN female 82 10.1 D G1511 GSM99451, GSM99450 GBM PN male 27 12.1 D G1516 GSM99555, GSM99554 GBM Mes female 41 147.3 A G1521 GSM99563, GSM99562 GBM PN female 23 146 A G1544 GSM99488, GSM99489 GBM Mes female 49 21.1 D G1656 GSM99440, GSM99441 GBM PN male 48 137.3 A G1667 GSM99447, GSM99446 GBM Mes male 44 84 D G1675 GSM99565, GSM99564 GBM Mes male 61 97.6 D G1681 GSM99589, GSM99588 GBM Mes male 40 132.4 A G1745 GSM99448, GSM99449 GBM PN female 42 111.4 A G1798 GSM99556, GSM99557 GBM Mes female 47 103.3 A G1900 GSM99485, GSM99484 GBM Prolif female 45 39.9 D G1902 GSM99442, GSM99443 GBM Mes female 56 46.4 D G1905 GSM99583, GSM99582 GBM PN male 75 55.6 D G2013 GSM99591, GSM99590 GBM Mes female 70 56.6 A G2015 GSM99445, GSM99444 GBM Mes male 78 56.6 A G2017 GSM99578, GSM99579 GBM Mes male 60 33.9 D G2028 GSM99531, GSM99530 GBM PN female 42 31.9 D G2029 GSM99533, GSM99532 GBM PN female 42 31.9 D G2067 GSM99538, GSM99539 GBM PN female 42 24 D G2068 GSM99540, GSM99541 GBM PN female 42 24 D G2079 GSM99486, GSM99487 GBM Mes male 64 42.6 A G2098 GSM99585, GSM99584 GBM Mes male 65 29 A G2158 GSM99472, GSM99473 GBM PN female 62 13.6 D G2166 GSM99559, GSM99558 GBM PN female 39 156.9 A G585 GSM99587, GSM99586 GBM PN female 63 43.1 D G597 GSM99534, GSM99535 GBM Mes male 35 1 D G604 GSM99572, GSM99573 GBM Mes male 66 26.4 D G636 GSM99476, GSM99477 GBM Prolif female 54 58.9 D G660 GSM99546, GSM99547 GBM PN female 75 16 D G697 GSM99436, GSM99437 GBM Mes female 64 50.9 D G706 GSM99453, GSM99452 GBM PN male 54 72.3 D G712 GSM99432, GSM99433 GBM Mes male 49 26.9 D G746 GSM99525, GSM99524 GBM PN male 52 6.1 D G749 GSM99462, GSM99463 GBM Mes male 39 7.6 D G782 GSM99577, GSM99576 GBM PN female 24 20 D G824 GSM99478, GSM99479 GBM PN female 50 26.6 D G839 GSM99481, GSM99480 GBM PN male 82 40.9 D G931 GSM99438, GSM99439 GBM Mes female 58 26 D G932 GSM99435, GSM99434 GBM PN female 18 14 D G938 GSM99536, GSM99537 GBM PN male 29 81.3 D G976 GSM99548, GSM99549 GBM Mes female 43 59.7 D G985 GSM99454, GSM99455 GBM PN female 76 8 D G996 GSM99527, GSM99526 GBM Prolif male 45 32 D MDA10334 GSM97053, GSM96953 GBM 0 PN male 38 210 A MDA11300 GSM97002, GSM97102 GBM 0 Prolif female 68 91 D MDA1153 S GBM 1 Unk male 12 MDA1351 GSM96999, GSM97099 GBM 1 Mes male 57 MDA13818 S GBM 0 Unk female 8 481 A MDA13921 GSM96979, GSM97079 GBM 0 Prolif female 60 32 D MDA13945 GSM96955, GSM97055 GBM 0 PN male 49 34 D MDA14085 GSM97089, GSM GBM 0 Mes male 49 106 D 96989 MDA14206 GSM97103, GSM97003 GBM 1 Prolif female 68 MDA14523 GSM97007, GSM97107 GBM 0 Prolif female 30 41 D MDA14558 GSM97073, GSM96973 GBM 0 Prolif male 76 52 D MDA15824 GSM97075, GSM96975 GBM 1 Mes male 43 MDA16713 GSM96960, GSM97060 GBM 1 Mes female 43 MDA16789 GSM96987, GSM97087 GBM 0 Mes male 34 33 D MDA17467 GSM97005, GSM97105 GBM 1 Mes male 72 MDA1765 GSM96952, GSM97052 GBM 0 Mes male 43 313 D MDA18395 S GBM 0 Unk male 12 170 A MDA20194 S GBM 0 Unk female 55.7 158 D MDA207 GSM97097, GSM96997 GBM 0 Prolif female 32 51 D MDA21226 GSM97080, GSM96980 GBM 0 Mes female 68 131 D MDA21537 GSM97067, GSM96967 GBM 0 Mes male 59 32 D MDA23057 GSM97010, GSM97110 GBM 0 Prolif male 57 70 D MDA23445 GSM97064, GSM96964 GBM 0 Mes male 49 59 D MDA23978 GSM97086, GSM96986 GBM 1 Prolif female 32 MDA24488 GSM97123, GSM97023 GBM 0 Mes male 43 47 D MDA24710 GSM97093, GSM96993 GBM 0 Mes male 54 125 D MDA24843 S GBM 0 Prolif male 17 120 D MDA24873 GSM96969, GSM97069 GBM 0 Prolif male 82 55 D MDA25266 GSM96985, GSM97085 GBM 0 Prolif male 48 111 D MDA25450 GSM97008, GSM97108 GBM 0 Mes male 39 53 D MDA2618 GSM96950, GSM97050 GBM 0 Mes male 60 131 D MDA28435 S GBM 2 Unk male 12 MDA28504 GSM97059, GSM96959 GBM 0 Prolif male 55 238 D MDA29621 GSM96978, GSM97078 GBM 0 Prolif male 57 242 A MDA30446 GSM97101, GSM97001 GBM 1 Mes male 57 MDA30617 GSM96976, GSM97076 GBM 0 Prolif male 54 97 D MDA31041 GSM97140, GSM97040 GBM 0 Mes male 54 53 D MDA31220 GSM97128, GSM97028 GBM 1 Mes male 54 MDA31237 GSM96951, GSM97051 GBM 0 Mes female 48 236 D MDA31472 GSM96998, GSM97098 GBM 1 Mes female 32 MDA32393 GSM97011, GSM97111 GBM 0 Mes male 50 3 D MDA33044 GSM97091, GSM96991 GBM 0 PN female 36 150 D MDA33054 GSM96996, GSM97096 GBM 0 Prolif female 43 12 D MDA33688 GSM97070, GSM96970 GBM 0 Prolif male 41 59 D MDA33825 GSM97141, GSM97041 GBM 0 Mes male 54.1 53.1 D MDA33859 GSM96977, GSM97077 GBM 0 Prolif male 40 95 D MDA34061 GSM96988, GSM97088 GBM 0 Mes male 55 57 D MDA34826 S GBM 1 Mes male 14 MDA35143 GSM96958, GSM97058 GBM 0 Mes male 57 181 D MDA35312 GSM96981, GSM97081 GBM 0 Mes male 47 77 D MDA36675 GSM96971, GSM97071 GBM 1 Prolif male 45 MDA36764 GSM96961, GSM97061 GBM 0 Mes male 50 311 D MDA37775 GSM96965, GSM97065 GBM 0 Mes male 48 97 D MDA38276 GSM96990, GSM97090 GBM 0 PN female 53 62 D MDA38490 GSM96992, GSM97092 GBM 0 Mes male 48 154 A MDA38805 GSM96984, GSM97084 GBM 0 Prolif female 34 16 D MDA38992 GSM97018, GSM97118 GBM 0 PN male 24 145 A MDA42116 GSM96966, GSM97066 GBM 0 Prolif male 44 33 D MDA42411 GSM97009, GSM97109 GBM 0 Prolif male 72 57 D MDA426 GSM97126, GSM97026 GBM 0 PN male 44 174 D MDA43291 S GBM 2 Mes male 14 MDA43849 GSM97094, GSM96994 GBM 0 Prolif female 32 39 D MDA4433 GSM97019, GSM97119 GBM 0 PN male 55 234 A MDA44442 GSM97062, GSM96962 GBM 0 Prolif male 54 62 D MDA47399 GSM97006, GSM97106 GBM 1 Mes female 72 MDA47813 GSM97100, GSM97000 GBM 0 Mes male 57 62 D MDA48078 GSM97104, GSM97004 GBM 0 Mes female 72 65 D MDA50100 GSM96972, GSM97072 GBM 0 Prolif female 43 210 A MDA50593 GSM97037, GSM97137 GBM 0 PN female 49 73 D MDA5060 GSM97057, GSM96957 GBM 1 Mes male 48 MDA53520 GSM96968, GSM97068 GBM 1 Prolif male 60 MDA54336 GSM97083, GSM96983 GBM 0 Prolif male 54 32 D MDA56075 GSM96974, GSM97074 GBM 0 Prolif male 29 123 D MDA56270 GSM96982, GSM97082 GBM 0 Mes female 48 56 D MDA5749 GSM97054, GSM96954 GBM 0 Prolif male 45 70 D MDA6326 GSM96995, GSM97095 GBM 0 Prolif female 58 79 D MDA7074 GSM97114, GSM97014 GBM 0 PN female 22.1 353.6 A MDA7379 GSM97144, GSM97044 GBM 1 PN female 49 MDA8277 GSM97063, GSM96963 GBM 0 PN male 34 203 D MDA834 GSM96956, GSM97056 GBM 1 PN male 34 MDA8662 S GBM 0 Mes male 14 42 D MDA9392 GSM97132, GSM97032 GBM 1 PN male 23 MDA9642 GSM97042, GSM97142 GBM 0 PN male 45 322 D MDAN1248 S Normal norm MDAN1486 S Normal norm MDAN1818 S Normal norm MDAN2512 S Normal norm MDAN3114 S Normal norm MDAN3116 S Normal norm MDAN3121 S Normal norm MDAN3122 S Normal norm N21A48 S Normal non-neoplastic norm epileptic plug N3886 S Normal non-neoplastic norm epileptic plug N7A41 S Normal non-neoplastic norm epileptic plug N88A_34 S Normal non-neoplastic norm epileptic plug N99A_36 S Normal non-neoplastic norm epileptic plug NJchip16 S Normal Normal norm tissue from GBM case SF0918 S GBM PN male 42.4 54.9 D SF0921 S GBM Mes female 54.5 80.3 D SF1166 S GBM Cerebrum: PN female 42.6 28.9 D Frontal lobe SF1167 S GBM Cerebrum: PN female 46.5 692.3 D Parietal lobe SF1198 S GBM Unk male 54.9 18.3 D SF1368 S GBM Cerebrum: Unk male 61.6 364.9 A Parietal lobe SF1388 S GBM Cerebrum: 1 PN female 29 24.7 D Frontal lobe SF1461 S GBM Cerebrum: Unk male 54.6 33.1 D Frontal lobe SF1475 S GBM Unk female 42 22.3 D SF1481 S GBM Cerebrum: PN female 44.2 49 D Parietal lobe SF1547 S GBM Cerebrum: Prolif female 35 33.6 D Frontal lobe SF1605 S GBM Cerebrum: Unk female 41 232 D Frontal Temporal lobe SF1653 S GBM Cerebrum: Unk male 51.3 58.3 D Parietal lobe SF1701 S GBM Cerebrum: PN male 66.4 503.4 D Frontal lobe SF1750 S GBM Cerebrum: Prolif female 45.1 67.7 D Temporal lobe SF1751 S GBM Cerebrum: PN female 38.3 70.4 D Frontal lobe SF1881 S GBM Cerebrum: Mes male 54 5.3 D Frontal lobe SF1913 S GBM Cerebrum: Mes male 47.6 82 D Temporal lobe SF2077 S GBM Cerebrum: Unk male 66.3 141.1 D Frontal lobe SF2159 S GBM Cerebrum: Unk male 43.2 47 D Frontal lobe SF2167 S GBM Cerebrum: PN male 25.5 145.7 D Temporal lobe SF2208 S GBM Cerebrum: Unk female 50 9.1 D Parietal lobe SF2315 S GBM Cerebrum: PN male 32.6 193 D Frontal lobe SF2399 S GBM Cerebrum: Unk male 38.9 50.4 D Frontal lobe SF2413 S GBM Cerebrum: PN female 50.1 226.6 D Frontal lobe SF2434 S GBM Cerebrum: Mes female 53.4 60.9 D Temporal lobe SF2560 S GBM Cerebrum: Unk male 51.7 40.3 D Frontal lobe SF2670 S GBM Cerebrum: Mes male 51.1 31.3 D Temporal lobe SF2703 S GBM Cerebrum: 1 PN male 27.6 37.7 D Temporal lobe SF2704 S GBM Cerebrum: Mes male 54.2 103.6 D Frontal lobe SF2737 S GBM Cerebrum: Mes male 50 38.7 D Temporal lobe SF2760 S GBM Cerebrum: 0 Mes male 47.5 97.1 D Frontal Temporal lobe SF2774 S GBM Cerebrum: Mes male 37.6 83 D Temporal lobe SF2777 S GBM Cerebrum: PN female 29.3 97.9 D Temporal lobe SF2894 S GBM Multifocal 0 Mes male 44.6 14 D SF2919 S GBM Cerebrum: Unk male 44.7 46.1 D Frontal lobe SF2935 S GBM Cerebrum: 1 Unk female 44.9 148 D Parietal lobe SF2969 S GBM Cerebrum: Unk female 34.9 24.9 D Frontal lobe SF3076 S GBM Cerebrum: Unk male 23.7 29 A Temporal lobe S = submitted to GEO

The following publications have additional clinical or molecular information for some of these tumors: Phillips H S. et al. (2006) Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer cell 9: 157-173. AND Freije W A. et al. (2004) Gene expression profiling of gliomas strongly predicts survival. Cancer research 64: 6503-6510.

Processing and Analysis of Microarray Data

The PI3K/AKT pathway integrates information on cellular environment, energy status, stress and developmental stage to regulate apoptosis, autophagy, translation, metabolism, stem cell function and cell cycle [20], [22]. This involves multiple sites of crosstalk with other pathways. To capture the full function the inventors generated a gene list that includes upstream and downstream gene products that directly or indirectly regulate or are regulated by AKT. This includes: (1) proteins or members of protein complexes that bind to, modify or regulate activity or subcellular localization of AKT (2) proteins or members of protein complexes phosphorylated or regulated by AKT, (3) proteins known to regulate or be regulated directly or indirectly by AKT (e.g. AKT through MDM2 regulates levels of TP53 protein). These genes were taken from: (1) a database of AKT interacting proteins (BOND [23]), (2) a database of AKT substrates (http://kinasource.co.uk/Database/substrateList.php) (3) evidence from Pubmed of phosphorylation by AKT (search term AKT, January 2008), (4) evidence from Pubmed that a gene regulates or is regulated by AKT either directly or indirectly (search term AKT, January 2008). Eliminating the genes with low variability across tumors within the discovery dataset left the 69 most variable genes used to classify AKT subgroups in the discovery dataset (Table 2). Five probes were not present in the validation dataset resulting in 64 of 69 AKT pathway genes applied during validation (Table 2). In accordance with the present invention, Table 2 lists non-limiting examples of the various genes that may be used to cluster AKT subgroups to diagnose and define GBM.

TABLE 2 AKT pathway gene classifiers used for the discovery and validation datasets discovery validation Akt pathway Akt pathway gene list gene list ACLY ACLY ATP citrate lyase AKT1 AKT1 V-akt murine thymoma viral oncogene homolog 1 ATXN1 ATXN1 Ataxin 1 BCL10 BCL10 B-cell CLL/lymphoma 10 CCND1 CCND1 Cyclin D1 CDC37 CDC37 Cell division cycle 37 CDKN1A CDKN1A Cyclin-dependent kinase inhibitor 1A (p21, Cip1) CDKN1B CDKN1B Cyclin-dependent kinase inhibitor 1B (p27, Kip1) CFD CFD Complement factor D (adipsin) CHEK1 CHEK1 Checkpoint kinase 1 EGFR EGFR Epidermal growth factor receptor EIF3B EIF3B Eukaryotic translation initiation factor 3, subunit B EIF3E EIF3E Eukaryotic translation initiation factor 3, subunit E EIF3G EIF3G Eukaryotic translation initiation factor 3, subunit G EIF3H EIF3H Eukaryotic translation initiation factor 3, subunit H EIF4EBP1 EIF4EBP1 Eukaryotic translation initiation factor 4E binding protein 1 EPAS1 EPAS1 Endothelial PAS domain protein 1 EZH2 EZH2 Enhancer of zeste homolog 2 (Drosophila) FGFR2 FGFR2 Fibroblast growth factor receptor 2 FGFR3 FGFR3 Fibroblast growth factor receptor 3 FOXO3 FOXO3 Forkhead box O3 FYN FYN FYN oncogene related to SRC, FGR, YES GAB1 GAB1 GRB2-associated binding protein 1 GAB2 GAB2 GRB2-associated binding protein 2 GRB10 GRB10 Growth factor receptor-bound protein 10 GSK3B GSK3B Glycogen synthase kinase 3 beta HIF1A HIF1A Hypoxia inducible factor 1, alpha subunit HSP90AB1 HSP90AB1 Heat shock protein 90 alpha (cytosolic), class B member 1 HSP90B1 HSP90B1 Heat shock protein 90 kDa beta (Grp94), member 1 INPP5D INPP5D Inositol polyphosphate-5-phosphatase, 145 kDa IRS1 IRS1 Insulin receptor substrate 1 IRS2 IRS2 Insulin receptor substrate 2 KDR KDR Kinase insert domain receptor (a type III receptor tyrosine kinase) KRAS KRAS V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog MAP3K5 MAP3K5 Mitogen-activated protein kinase kinase kinase 5 MAPK8IP1 MAPK8IP1 Mitogen-activated protein kinase 8 interacting protein 1 NRAS NRAS Neuroblastoma RAS viral (v-ras) oncogene homolog PALLD PALLD Palladin, cytoskeletal associated protein PDGFA PDGFA Platelet-derived growth factor alpha polypeptide PDGFC PDGFC Platelet derived growth factor C PDGFD PDGFD Platelet derived growth factor D PDGFRB PDGFRB Platelet-derived growth factor receptor, beta polypeptide PDK1 PDK1 3-phosphoinositide dependent protein kinase-1 PHLPP PHLPP1 PH domain and leucine rich repeat protein phosphatase 1 PIK3C2B PIK3C2B Phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta PIK3CA PIK3CA Phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha PIK3R1 PIK3R1 Phosphoinositide-3-kinase, regulatory subunit 1 (alpha) PKD2 PKD2 Polycystic kidney disease 2 (autosomal dominant) PKN2 PKN2 Protein kinase N2 PPARGC1A PPARGC1A Peroxisome proliferator-activated receptor gamma, coactivator 1 alpha PPP2R1A PPP2R1A Protein phosphatase 2, regulatory subunit A, alpha PPP2R2B PPP2R2B Protein phosphatase 2, regulatory subunit B, beta RAF1 RAF1 V-raf-1 murine leukemia viral oncogene homolog 1 SFRS1 SRSF1 Serine/arginine-rich splicing factor 1 SORBS2 SORBS2 Sorbin and SH3 domain containing 2 SSB SSB Sjogren syndrome antigen B (autoantigen La) SYK SYK Spleen tyrosine kinase TP53 TP53 Tumor protein p53 TRIB3 TRIB3 Tribbles homolog 3 (Drosophila) TSC1 TSC1 Tuberous sclerosis 1 TSC2 TSC2 Tuberous sclerosis 2 TWIST1 TWIST1 Twist basic helix-loop-helix transcription factor 1 VIM VIM Vimentin WNK1 WNK1 WNK lysine deficient protein kinase 1 AKT1S1 AKT1 substrate 1 (proline-rich) IGF2 Insulin-like growth factor 2 (somatomedin A) PPP2R2C Protein phosphatase 2, regulatory subunit B, gamma RICTOR RPTOR independent companion of MTOR, complex 2 YBX1 Y box binding protein 1

The inventors isolated patient subgroups in the discovery dataset using RMA normalized and median centered data [24]. The inventors applied consensus k-means clustering with the Pearson's correlation coefficient as the similarity (1-distance) and complete linkage with 10,000 iterations using a sub-sampling ratio of 0.8. The inventors then plotted the consensus distribution function (CDF) to find the optimal number of AKT subgroups [25]. Silhouette width values were computed for each sample [26] and only samples with a positive silhouette width were used in further analyses.

The inventors isolated AKT subgroups in the TCGA validation dataset using raw data preprocessed as described for the discovery dataset. TCGA samples were mapped onto AKT subgroups in the discovery dataset by adapting the k means clustering algorithm. First, the inventors found boundaries for each AKT subgroup in the discovery set by calculating the pairwise correlation coefficients between all samples within a subgroup. The minimum pairwise correlation coefficient was used as the lower boundary for each subgroup. TCGA samples were classified by computing the correlation coefficient between each TCGA and GBM195 sample. TCGA samples were assigned to an AKT subgroup if the average pairwise correlation coefficient with members of the group was greater than the lower boundary of that group. Ties were resolved by selecting the closest cluster.

Analysis of GO Terms

Conventional Gene Ontology (GO) enrichment analysis was dominated by generic GBM biological processes; therefore the inventors used a single-sample approach analogous to the method used by Verhaak and Barbie [10]. To identify GO biological processes enriched within each individual sample the inventors applied the hypergeometric test with Benjamini and Hochberg's correction on all expressed genes (using a two-fold change threshold from the median to determine up- and down-regulated genes). Neurodevelopmental terms enriched in >20% of tumors were considered for analysis.

Analysis of aCGH Data

The GISTIC algorithm [27] was applied to the 456 TCGA samples with copy number information and results visualized using the Integrated Genomic Viewer (IGV) [28] to find copy number alterations (CNA) in the validation set. Broad copy number alterations in the discovery dataset were found as described previously [29] using a customized version of the Sanger CNV database [http://www.sanger.ac.uk/research/areas/humangenetics/cnv/]. For experiments that compare broad CNA in the discovery and validation dataset the inventors identified broad copy number alterations in the validation dataset as follows. Briefly, the inventors found the average q value (generated from the GISTIC algorithm) for 15 genes spaced evenly across the region of interest. If >50% of genes had a q value less than expected by chance after correcting for multiple testing (q<0.25), that region was called as a copy number alteration.

Reverse Phase Protein Arrays

Level 3 (median centered, normalized, Z transformed) reverse phase protein array (RPPA) data was downloaded from the cBio Cancer Genomics Portal (http://www.cbioportal.org/public-portal/). One hundred and eighty six of the 215 tumors with RPPA data could be assigned to an AKT class and were used for analysis. Correlation coefficients between two antibodies against the same protein were high indicating adequate antibody specificity and pre-processing of data (Pearson correlation coefficient=0.83-0.98 for antibody pairs (GSK3A/B pS9/21, MAPK1, FOXO3, GATA3, 5338 p-RAF1).

Statistics

Differences between one subgroup and the rest were assessed using the F test for clinical variables and the likelihood ratio test for categorical variables. The Bonferroni method [30] was applied to correct for multiple hypotheses. The inventors applied the Tukey HSD test to find pairwise differences between groups and correct for multiple comparisons [31]. Survival differences between subgroups were assessed using the Chi-squared test. Age was added to build a multivariate Cox model. For survival comparisons of BCNU/CCNU treatment between subgroups there were not enough observations to correct for age. After deleting all observations younger than 45, survival was no longer related to age. Significance was then determined using log rank. The Pearson goodness-of-fit test was used to assess the null hypothesis that proportions of G-CIMP tumors by subgroup and recurrent tumors by subgroup are equal to the proportions for all tumors by subgroup. P-values for these tests were calculated by Monte Carlo simulation since the counts of tumors by subgroup were too small to apply the large sample chi-square approximation. If the null hypothesis was rejected, then standardized residuals were used to determine which subgroups showed significant differences.

Example 2: AKT Pathway Genes Define 5 Prognostic Subgroups in Glioblastoma

AKT Pathway Gene Expression Divides GBM into at Least Six Subgroups

The inventors investigated AKT pathway variations in GBM by developing a list of AKT pathway genes (Table 2) then applying consensus clustering for the number of clusters k=2 to 10 (FIG. 9; FIG. 1A shows results for k=5 to 8). The inventors evaluated cluster stability using the consensus cumulative distribution function (CDF) plot of the consensus index (FIG. 1C) [25]. Cluster stability increased for k=2 to 6 but not appreciably for k>6 (FIG. 1C); suggesting six is the optimum number of GBM AKT subgroups. Silhouette width values were computed for each sample [26] (FIG. 1B) and samples with a positive silhouette width were selected for further analyses.

The inventors aim to have a classification system where clinical differences are maximized. Here, the inventors investigated how survival of patient subgroups varies with k. FIG. 1D plots the corrected p value between the longest and shortest surviving subgroups for each k. p values were low for k=3 and 6; k=6 was the lowest (FIG. 1D). This supports the CDF results selecting 6 clusters. The 6 consensus k-means subgroups were named AKT cluster 1 (AKT C1; AKT subgroup 1), AKT proneural (AKT PN; AKT subgroup 2), AKT mesenchymal (AKT MES; AKT subgroup 3), AKT classical (AKT CLAS; AKT subgroup 4), AKT secondary-like (AKT SL; AKT subgroup 5) and AKT proliferative (AKT PROLIF; AKT subgroup 6) based on their molecular and clinical features and prior naming [4], [32].

Validation of AKT Subgroups in an Independent Dataset

The inventors next validated AKT subgroups in an independent dataset of non-overlapping samples. TCGA samples were mapped onto discovery AKT subgroups by assigning a sample to the closest Akt subtype, as described in the methods section. Only two samples were assigned to AKT subgroup C1, therefore this subgroup was dropped from all further analysis. FIGS. 2A-2B compare AKT pathway gene expression in the discovery (FIG. 2A) and validation (FIG. 2B) sets. It shows the pattern of expression of AKT pathway genes within subgroups is similar in both datasets. Interestingly, the PN subgroup in both datasets contained all non-neoplastic samples (not shown). The inventors examined expression of AKT pathway genes in subgroups (FIG. 10 or Table 6). These data show AKT classes arise from complex patterns of gene expression in subgroups. It did not point to a role for a specific part of the AKT pathway within any subgroup.

The inventors next investigated correspondence between copy number alterations (CNA) in AKT subgroups from discovery (FIG. 2C) and validation (FIG. 2D) datasets. The PN subgroup was omitted since it had no CNA information in the discovery dataset. CNA within subgroups were similar in the discovery and validation datasets: a high percentage of tumors with 7 gain/10 loss occurred in every subgroup except SL, the SL subgroup had greater frequency of 19q loss and the CLAS subgroup had increased gain of chr19q relative to the rest. Therefore all subgroup-associated trends in CNA within the discovery dataset were recapitulated in the validation dataset.

TCGA, Phillips and G-CIMP Subgroups Distribute Non-Randomly in AKT Subgroups

Phillips, TCGA and G-CIMP subgroups distributed non-randomly in AKT subgroups (FIG. 3; FIGS. 12 and 13). There was a tendency for AKT subtyping to split each Phillips subgroup in two. The AKT PN and SL subtypes were significantly enriched in the Phillips PN subtype (FIG. 3, FIGS. 12A and 12B; p<0.5 Bonferroni corrected). The AKT MES and CLAS subtypes were significantly enriched in Phillips MES subtype (FIG. 3, FIGS. 12A and 12B, p<0.5; Bonferroni corrected). The AKT PROLIF subtype was significantly enriched in the Phillips PROLIF subtype (FIG. 3, FIGS. 12A and 12B; p<0.5; Bonferroni corrected). The enrichment of Phillips PROLIF tumors in AKT C1 subtype did not reach significance. AKT subgroups had less concordance with TCGA subgroups [10]. AKT SL and PROLIF subtypes were significantly enriched in TCGA PN subtype; while AKT MES and CL subgroups were enriched in the TCGA MES and CL subtype, respectively (FIG. 3, FIGS. 13A and 13B; p<0.5; Bonferroni corrected). The AKT PN subtype was a mixture of all the TCGA subgroups. The AKT SL and PROLIF subgroups contained the majority of G-CIMP tumors (FIG. 3). Taken together these data show AKT classification divides existing subgroups further.

Patients in the SL Subgroup are Younger and have Longer Survival

AKT subgroups have different clinical characteristics (FIGS. 4B and D; FIGS. 12 and 13). SL patients in the discovery dataset had longer median survival (3.9 vs. 1.05 yrs.; p=0.0005; FIG. 4B; SL vs. the rest) and were younger (median age=38 vs. 49; SL vs. total; p=0.05 using Tukey HSD test to correct for multiple comparisons; FIGS. 12A and 12B). After adjusting for age in Cox multivariate analysis, SL status remained a significant predictor of survival (p=0.027; SL vs. the rest). The PROLIF subgroup had statistically significant shorter survival than the rest (0.75 vs. 1.25 yrs.; p=0.0029; FIG. 4B) although age of these patients was not different than all patients (median age=49 vs. 49 years; PROLIF vs. total; FIGS. 12A and 12B). Although the magnitude was diminished, a similar trend was observed for SL patients in the validation dataset for survival (1.67 vs. 1.1 yrs.; p=0.003 SL vs. rest; FIG. 4D) and age (median age=49 vs. 59 yrs.; p=0.07; SL vs. total, FIGS. 13A and 13B) although the age difference was not statistically significant. In comparison, patient subgroups defined using Phillips (FIG. 4A) and TCGA (FIG. 4C) methods using the same database have no statistically significant differences in survival.

Consistent with the less aggressive character of SL tumors, there was a trend toward decreased endothelial proliferation (46% vs. 66%; p=0.017 vs. rest; uncorrected), and palisading necrosis (10% vs. 51%; p=0.07 vs. rest; uncorrected) in the validation dataset (FIGS. 13A and 13B). There were similar trends in the discovery set although they also did not reach significance (FIGS. 12A and 12B). Taken together these data show subgroups in the discovery and validation datasets have similar clinical features. It also shows AKT subtypes have distinct clinical characteristics.

Evidence AKT Subtyping is a Predictive Marker for Sensitivity to BCNU/CCNU

Survival differences between subgroups suggest AKT subtypes are either prognostic or predictive (forecasts tumor aggressiveness or response to therapy, respectively). Since AKT influences response to chemotherapy [33], while not wishing to be bound by any theory, the inventors believe AKT subgroups are predictive markers. Indeed, TCGA SL patients treated with BCNU or CCNU had longer median survival than those receiving other treatments (FIG. 5; median survival=5.8 vs. 1.05 years; p=0.03 after correcting for age; log rank). Those receiving BCNU or CCNU were older and had less IDH1 mutations than those that didn't (median age=54 vs. 49 years; % with IDH1 mutations=17% vs. 32%; with vs. without BCNU/CCNU respectively); indicating age and IDH1 mutation status do not account their increased survival. This finding indicates patients in the SL subgroup are sensitive to BCNU and CCNU.

Subgroups have Distinct Genomic Alterations

The inventors used TCGA data to investigate how molecular alterations partition in subgroups. All subgroups had unique broad (FIG. 6A; FIG. 11) and/or focal (FIGS. 14 and 15) DNA CNA. The CLAS subtype was enriched in broad CNA previously associated with more aggressive tumors such as loss of chromosome regions 6q and gain of 19q and 20q [34] (FIG. 6A). The SL subtype was enriched in broad CNA associated with better prognosis (loss of 19q; FIG. 6A) [34]. Each subgroup had unique focal CNA (FIGS. 14 and 15). This data shows AKT subtyping groups tumors with similar molecular characteristics.

An integrated analysis of mutations, CNA and mRNA expression in glioma-associated genes shows some AKT subgroups had similar features as TCGA subgroups (FIG. 6B). The AKT CLAS subgroup was significantly enriched in alterations in EGFR and CDKN2A similar to TCGA CLAS subgroup [10]. The AKT MES subtype was characterized by mutations in NF1 and RB1 and increased mRNA for the mesenchymal marker, MET, similar to the TCGA MES subgroup [10], although these did not reach statistical significance. The SL subtype was enriched in IDH1 mutations (42% vs 3% SL vs. rest) and GCIMP (47% vs. 4%; SL vs. rest) although only the enrichment in IDH1 mutant tumors was significant. The PROLIF subtype was also slightly enriched in IDH1 mutations (11%) in this dataset containing 218 validated samples. However that dropped to 7% when considering all TCGA tumors with IDH1 mutation information (not shown). Both the SL and PROLIF subgroups were also enriched in alterations found more frequently in secondary tumors including TP53 mutations and increased mRNA and CN gains for PDGFRA. The PROLIF was distinguished from SL subtype by an increase in mutations and copy number alterations in EGFR and CDKN2A (FIG. 6B) and enrichment in recurrent tumors (18% vs 8%; PROLIF vs rest; FIGS. 13A and 13B). Genomic alterations in other RTK/RAS/PI3K/AKT pathway members were either not significantly enriched in any subgroup (PTEN, PIK3R1, MET, SPRY2; FIG. 6B) or the frequency was too low to evaluate (ERBB2, KRAS, NRAS, HRAS, PIK3CA, FOXO1, FOXO3, AKT1, AKT2, AKT3; not shown); although MET mRNA was enriched and SPRY2 mRNA was low in the MES and CLAS subtypes, respectively (FIG. 6B). Taken together these data suggest involvement of oncogenic and tumor suppressor pathways can differ between subgroups.

Subgroups have Distinct Patterns of Expression for PI3K/AKT/mTOR Components

The inventors find subgroups have distinct patterns of expression of mRNA (FIG. 7A), protein and phospho-proteins (FIG. 7B) for PI3K/AKT/mTOR pathway components. The most notable patterns were in the MES and SL subgroups. The MES subtype had decreased expression for inhibitors of mTOR, AKT and PI3K (TSC2 and p-AMPK protein; TSC1, TSC2, PHLPP1, PHLPP2 and PI3KR1 message). Consistent with increased activity of the AKT/mTOR/S6 axis, this subgroup also had elevated p-S6 (FIG. 7B) and a high positive correlation between p-AKT and p-S6 (FIG. 7C). The long surviving SL subgroup had the opposite pattern of expression; high expression of AKT and mTOR inhibitors (FIGS. 7A and B), decreased expression of pS6 (FIG. 7B) and lower correlation between pAKT and pS6 (FIG. 7C). The inventors' proposed pathway map for the MES and SL subgroups (7D) based on this data posits how expression of pathway inhibitors affects output of the AKT/mTOR/S6 axis. This data indicates subgroups will have different sensitivities to pathway inhibitors.

GO Terms Suggest Subgroups have a Different Dominant Biological Process and Cell of Origin

The inventors used Gene Ontology (GO) to investigate the biological role of genes expressed in tumors and how terms partition in subgroups. Each subgroup, except CLAS, had a high percentage of tumors with functionally related terms that suggested a different dominate biological process (Table 3). The CLAS subgroup had a mixture of terms. Each subgroup also had GO terms associated with neurodevelopment (Table 3; highlighted with bolded text; summarized in FIG. 8B). The PN and CLAS subgroups had only terms associated with neurogenesis suggesting a committed neural precursor cell of origin. The MES, SL and PROLIF subgroups had terms associated with both neuro- and glio-genesis suggesting a stem cell or early uncommitted progenitor cell of origin. These data suggest the cell of origin and dominant biological process can differ in subgroups.

TABLE 3 GO term analysis of genes differentially expressed in subgroups Proportion Biological of Samples Process Biological Process Name C1 (2 Samples) 100%  GO:0000087 M phase of mitotic cell cycle 100%  GO:0000236 mitotic prometaphase 100%  GO:0000278 mitotic cell cycle 100%  GO:0000279 M phase 100%  GO:0000280 nuclear division 100%  GO:0007067 mitosis 100%  GO:0022402 cell cycle process 100%  GO:0022403 cell cycle phase 100%  GO:0048285 organelle fission 50%  GO:0006336 DNA replication-independent nucleosome assembly 50%  GO:0007051 spindle organization 50%  GO:0007059 chromosome segregation 50%  GO:0007091 mitotic metaphase/anaphase transition 50%  GO:0007094 mitotic cell cycle spindle assembly checkpoint 50%  GO:0030071 regulation of mitotic metaphase/anaphase transition 50%  GO:0031055 chromatin remodeling at centromere 50%  GO:0031577 spindle checkpoint 50%  GO:0034080 CenH3-containing nucleosome assembly at centromere 50%  GO:0034724 DNA replication-independent nucleosome organization 50%  GO:0043486 histone exchange 50%  GO:0045841 negative regulation of mitotic metaphase/anaphase transition 50%  GO:0046826 negative regulation of protein export from nucleus 50%  GO:0051301 cell division 50%  GO:0051983 regulation of chromosome segregation 50%  GO:0071173 spindle assembly checkpoint 50%  GO:0071174 mitotic cell cycle spindle checkpoint PN (30 Samples) 100%  GO:0001505 regulation of neurotransmitter levels 100%  GO:0003001 generation of a signal involved in cell-cell signaling 100%  GO:0006836 neurotransmitter transport 100%  GO:0007268 synaptic transmission 100%  GO:0007269 neurotransmitter secretion 100%  GO:0014047 glutamate secretion 100%  GO:0019226 transmission of nerve impulse 100%  GO:0023061 signal release 100%  GO:0035637 multicellular organismal signaling 100%  GO:0048489 synaptic vesicle transport 97%  GO:0007267 cell-cell signaling 97%  GO:0031644 regulation of neurological system process 97%  GO:0050877 neurological system process 97%  GO:0051969 regulation of transmission of nerve impulse 93%  GO:0050804 regulation of synaptic transmission 90%  GO:0007399 nervous system development 90%  GO:0016079 synaptic vesicle exocytosis 87%  GO:0032940 secretion by cell 83%  GO:0048167 regulation of synaptic plasticity 80%  GO:0022008 neurogenesis 80%  GO:0030182 neuron differentiation 77%  GO:0048667 cell morphogenesis involved in neuron differentiation 77%  GO:0048699 generation of neurons 77%  GO:0048812 neuron projection morphogenesis 73%  GO:0007409 axonogenesis 73%  GO:0031175 neuron projection development 73%  GO:0048666 neuron development 67%  GO:0000904 cell morphogenesis involved in differentiation 63%  GO:0007611 learning or memory 63%  GO:0030030 cell projection organization 63%  GO:0048858 cell projection morphogenesis 60%  GO:0003008 system process 60%  GO:0032990 cell part morphogenesis 60%  GO:0048488 synaptic vesicle endocytosis 57%  GO:0042391 regulation of membrane potential 57%  GO:0046903 secretion 57%  GO:0050890 cognition 53%  GO:0007612 learning 50%  GO:0006887 exocytosis 50%  GO:0007214 gamma-aminobutyric acid signaling pathway 47%  GO:0044057 regulation of system process 47%  GO:0048168 regulation of neuronal synaptic plasticity 47%  GO:0050773 regulation of dendrite development 43%  GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 43%  GO:0007610 behavior 40%  GO:0000902 cell morphogenesis 40%  GO:0051899 membrane depolarization 40%  GO:0060333 interferon-gamma-mediated signaling pathway 37%  GO:0090072 positive regulation of sodium ion transport via voltage-gated sodium channel activity 33%  GO:0010243 response to organic nitrogen 33%  GO:0060627 regulation of vesicle-mediated transport 30%  GO:0007272 ensheathment of neurons 30%  GO:0008366 axon ensheathment 30%  GO:0071346 cellular response to interferon-gamma 27%  GO:0017157 regulation of exocytosis 27%  GO:0032989 cellular component morphogenesis 27%  GO:0034341 response to interferon-gamma 27%  GO:0042552 myelination 23%  GO:0001508 regulation of action potential 23%  GO:0019228 regulation of action potential in neuron 23%  GO:0051592 response to calcium ion 23%  GO:0055082 cellular chemical homeostasis 20%  GO:0006873 cellular ion homeostasis 20%  GO:0010975 regulation of neuron projection development 17%  GO:0006821 chloride transport 17%  GO:0010970 microtubule-based transport 17%  GO:0048468 cell development 13%  GO:0006413 translational initiation 13%  GO:0006415 translational termination 13%  GO:0006614 SRP-dependent cotranslational protein targeting to membrane 13%  GO:0008088 axon cargo transport 13%  GO:0015698 inorganic anion transport 13%  GO:0019080 viral genome expression 13%  GO:0019083 viral transcription 13%  GO:0019725 cellular homeostasis 13%  GO:0043241 protein complex disassembly 13%  GO:0043624 cellular protein complex disassembly 13%  GO:0045047 protein targeting to ER 13%  GO:0060079 regulation of excitatory postsynaptic membrane potential 13%  GO:0060314 regulation of ryanodine-sensitive calcium-release channel activity 13%  GO:0070972 protein localization in endoplasmic reticulum 13%  GO:0072599 establishment of protein localization in endoplasmic reticulum 10%  GO:0002480 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent 10%  GO:0006414 translational elongation 10%  GO:0006612 protein targeting to membrane 10%  GO:0006613 cotranslational protein targeting to membrane 10%  GO:0009263 deoxyribonucleotide biosynthetic process 10%  GO:0010001 glial cell differentiation 10%  GO:0014075 response to amine stimulus 10%  GO:0019058 viral infectious cycle 10%  GO:0022411 cellular component disassembly 10%  GO:0023052 signaling 10%  GO:0030001 metal ion transport 10%  GO:0030168 platelet activation 10%  GO:0030705 cytoskeleton-dependent intracellular transport 10%  GO:0031344 regulation of cell projection organization 10%  GO:0031646 positive regulation of neurological system process 10%  GO:0032984 macromolecular complex disassembly 10%  GO:0034623 cellular macromolecular complex disassembly 10%  GO:0042063 gliogenesis 10%  GO:0048709 oligodendrocyte differentiation 10%  GO:0050805 negative regulation of synaptic transmission 10%  GO:0050806 positive regulation of synaptic transmission 10%  GO:0051049 regulation of transport 10%  GO:0051823 regulation of synapse structural plasticity 10%  GO:0051971 positive regulation of transmission of nerve impulse 10%  GO:0071417 cellular response to organic nitrogen 10%  GO:0071418 cellular response to amine stimulus 10%  GO:0071845 cellular component disassembly at cellular level 10%  GO:0072594 establishment of protein localization to organelle 7% GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 7% GO:0002495 antigen processing and presentation of peptide antigen via MHC class II 7% GO:0006820 anion transport 7% GO:0007154 cell communication 7% GO:0014003 oligodendrocyte development 7% GO:0015800 acidic amino acid transport 7% GO:0016081 synaptic vesicle docking involved in exocytosis 7% GO:0017156 calcium ion-dependent exocytosis 7% GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II 7% GO:0022010 central nervous system myelination 7% GO:0022415 viral reproductive process 7% GO:0030224 monocyte differentiation 7% GO:0031111 negative regulation of microtubule polymerization or depolymerization 7% GO:0032291 axon ensheathment in central nervous system 7% GO:0034340 response to type I interferon 7% GO:0042274 ribosomal small subunit biogenesis 7% GO:0043090 amino acid import 7% GO:0043092 L-amino acid import 7% GO:0048169 regulation of long-term neuronal synaptic plasticity 7% GO:0060337 type I interferon-mediated signaling pathway 7% GO:0065008 regulation of biological quality 7% GO:0071229 cellular response to acid 7% GO:0071357 cellular response to type I interferon 3% GO:0000956 nuclear-transcribed mRNA catabolic process 3% GO:0001101 response to acid 3% GO:0001504 neurotransmitter uptake 3% GO:0001766 membrane raft polarization 3% GO:0001915 negative regulation of T cell mediated cytotoxicity 3% GO:0002237 response to molecule of bacterial origin 3% GO:0002246 wound healing involved in inflammatory response 3% GO:0002250 adaptive immune response 3% GO:0002252 immune effector process 3% GO:0002253 activation of immune response 3% GO:0002376 immune system process 3% GO:0002429 immune response-activating cell surface receptor signaling pathway 3% GO:0002443 leukocyte mediated immunity 3% GO:0002449 lymphocyte mediated immunity 3% GO:0002455 humoral immune response mediated by circulating immunoglobulin 3% GO:0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 3% GO:0002474 antigen processing and presentation of peptide antigen via MHC class I 3% GO:0002478 antigen processing and presentation of exogenous peptide antigen 3% GO:0002479 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent 3% GO:0002682 regulation of immune system process 3% GO:0002683 negative regulation of immune system process 3% GO:0002684 positive regulation of immune system process 3% GO:0002685 regulation of leukocyte migration 3% GO:0002686 negative regulation of leukocyte migration 3% GO:0002688 regulation of leukocyte chemotaxis 3% GO:0002689 negative regulation of leukocyte chemotaxis 3% GO:0002694 regulation of leukocyte activation 3% GO:0002696 positive regulation of leukocyte activation 3% GO:0002757 immune response-activating signal transduction 3% GO:0002764 immune response-regulating signaling pathway 3% GO:0002768 immune response-regulating cell surface receptor signaling pathway 3% GO:0006401 RNA catabolic process 3% GO:0006402 mRNA catabolic process 3% GO:0006412 translation 3% GO:0006605 protein targeting 3% GO:0006826 iron ion transport 3% GO:0006886 intracellular protein transport 3% GO:0006935 chemotaxis 3% GO:0006952 defense response 3% GO:0006954 inflammatory response 3% GO:0006955 immune response 3% GO:0006956 complement activation 3% GO:0006958 complement activation, classical pathway 3% GO:0006959 humoral immune response 3% GO:0007026 negative regulation of microtubule depolymerization 3% GO:0007417 central nervous system development 3% GO:0009265 2′-deoxyribonucleotide biosynthetic process 3% GO:0009607 response to biotic stimulus 3% GO:0009611 response to wounding 3% GO:0009615 response to virus 3% GO:0009617 response to bacterium 3% GO:0009914 hormone transport 3% GO:0015682 ferric iron transport 3% GO:0015813 L-glutamate transport 3% GO:0015988 energy coupled proton transport, against electrochemical gradient 3% GO:0015991 ATP hydrolysis coupled proton transport 3% GO:0016064 immunoglobulin mediated immune response 3% GO:0016188 synaptic vesicle maturation 3% GO:0019724 B cell mediated immunity 3% GO:0019882 antigen processing and presentation 3% GO:0019884 antigen processing and presentation of exogenous antigen 3% GO:0021675 nerve development 3% GO:0021782 glial cell development 3% GO:0030198 extracellular matrix organization 3% GO:0030199 collagen fibril organization 3% GO:0030334 regulation of cell migration 3% GO:0030534 adult behavior 3% GO:0030595 leukocyte chemotaxis 3% GO:0031102 neuron projection regeneration 3% GO:0031114 regulation of microtubule depolymerization 3% GO:0031294 lymphocyte costimulation 3% GO:0031295 T cell costimulation 3% GO:0031345 negative regulation of cell projection organization 3% GO:0031580 membrane raft distribution 3% GO:0031645 negative regulation of neurological system process 3% GO:0032101 regulation of response to external stimulus 3% GO:0032103 positive regulation of response to external stimulus 3% GO:0032496 response to lipopolysaccharide 3% GO:0033124 regulation of GTP catabolic process 3% GO:0033365 protein localization to organelle 3% GO:0033572 transferrin transport 3% GO:0034097 response to cytokine stimulus 3% GO:0040012 regulation of locomotion 3% GO:0042330 taxis 3% GO:0042493 response to drug 3% GO:0042590 antigen processing and presentation of exogenous peptide antigen via MHC class I 3% GO:0042592 homeostatic process 3% GO:0043062 extracellular structure organization 3% GO:0043087 regulation of GTPase activity 3% GO:0043200 response to amino acid stimulus 3% GO:0043242 negative regulation of protein complex disassembly 3% GO:0043368 positive T cell selection 3% GO:0045059 positive thymic T cell selection 3% GO:0045061 thymic T cell selection 3% GO:0045087 innate immune response 3% GO:0045163 clustering of voltage-gated potassium channels 3% GO:0045663 positive regulation of myoblast differentiation 3% GO:0045730 respiratory burst 3% GO:0045766 positive regulation of angiogenesis 3% GO:0046928 regulation of neurotransmitter secretion 3% GO:0048002 antigen processing and presentation of peptide antigen 3% GO:0048015 phosphatidylinositol-mediated signaling 3% GO:0048017 inositol lipid-mediated signaling 3% GO:0048583 regulation of response to stimulus 3% GO:0048584 positive regulation of response to stimulus 3% GO:0048678 response to axon injury 3% GO:0048731 system development 3% GO:0048878 chemical homeostasis 3% GO:0050776 regulation of immune response 3% GO:0050778 positive regulation of immune response 3% GO:0050795 regulation of behavior 3% GO:0050801 ion homeostasis 3% GO:0050851 antigen receptor-mediated signaling pathway 3% GO:0050863 regulation of T cell activation 3% GO:0050865 regulation of cell activation 3% GO:0050867 positive regulation of cell activation 3% GO:0050870 positive regulation of T cell activation 3% GO:0050920 regulation of chemotaxis 3% GO:0050921 positive regulation of chemotaxis 3% GO:0051050 positive regulation of transport 3% GO:0051056 regulation of small GTPase mediated signal transduction 3% GO:0051129 negative regulation of cellular component organization 3% GO:0051239 regulation of multicellular organismal process 3% GO:0051249 regulation of lymphocyte activation 3% GO:0051665 membrane raft localization 3% GO:0051707 response to other organism 3% GO:0051938 L-glutamate import 3% GO:0051970 negative regulation of transmission of nerve impulse 3% GO:0060078 regulation of postsynaptic membrane potential 3% GO:0060326 cell chemotaxis 3% GO:0060384 innervation 3% GO:0070098 chemokine-mediated signaling pathway 3% GO:0071205 protein localization to juxtaparanode region of axon 3% GO:0071219 cellular response to molecule of bacterial origin 3% GO:0071222 cellular response to lipopolysaccharide 3% GO:0071230 cellular response to amino acid stimulus 3% GO:0071402 cellular response to lipoprotein particle stimulus 3% GO:0072012 glomerulus vasculature development 3% GO:0072239 metanephric glomerulus vasculature development 3% GO:0090025 regulation of monocyte chemotaxis 3% GO:2000145 regulation of cell motility 3% GO:2000300 regulation of synaptic vesicle exocytosis MES (34 Samples) 68%  GO:0006952 defense response 68%  GO:0009611 response to wounding 65%  GO:0006955 immune response 65%  GO:0045087 innate immune response 62%  GO:0002376 immune system process 62%  GO:0051707 response to other organism 59%  GO:0006954 inflammatory response 59%  GO:0007155 cell adhesion 59%  GO:0009607 response to biotic stimulus 59%  GO:0022610 biological adhesion 56%  GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 56%  GO:0009617 response to bacterium 56%  GO:0034341 response to interferon-gamma 53%  GO:0002250 adaptive immune response 53%  GO:0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 53%  GO:0006956 complement activation 53%  GO:0006959 humoral immune response 53%  GO:0016064 immunoglobulin mediated immune response 53%  GO:0019724 B cell mediated immunity 53%  GO:0030198 extracellular matrix organization 53%  GO:0043062 extracellular structure organization 53%  GO:0045765 regulation of angiogenesis 53%  GO:0050900 leukocyte migration 50%  GO:0002237 response to molecule of bacterial origin 50%  GO:0002252 immune effector process 50%  GO:0002253 activation of immune response 50%  GO:0006950 response to stress 50%  GO:0032496 response to lipopolysaccharide 50%  GO:0034097 response to cytokine stimulus 50%  GO:0040011 locomotion 50%  GO:0071346 cellular response to interferon-gamma 47%  GO:0001568 blood vessel development 47%  GO:0001944 vasculature development 47%  GO:0002443 leukocyte mediated immunity 47%  GO:0016477 cell migration 47%  GO:0030199 collagen fibril organization 47%  GO:0032101 regulation of response to external stimulus 47%  GO:0043200 response to amino acid stimulus 47%  GO:0050776 regulation of immune response 44%  GO:0001101 response to acid 44%  GO:0002449 lymphocyte mediated immunity 44%  GO:0002684 positive regulation of immune system process 44%  GO:0006928 cellular component movement 44%  GO:0006935 chemotaxis 44%  GO:0009605 response to external stimulus 44%  GO:0010033 response to organic substance 44%  GO:0030334 regulation of cell migration 44%  GO:0042060 wound healing 44%  GO:0042330 taxis 44%  GO:0050778 positive regulation of immune response 41%  GO:0002576 platelet degranulation 41%  GO:0002682 regulation of immune system process 41%  GO:0006958 complement activation, classical pathway 41%  GO:0010243 response to organic nitrogen 41%  GO:0022603 regulation of anatomical structure morphogenesis 41%  GO:0040017 positive regulation of locomotion 41%  GO:0042221 response to chemical stimulus 41%  GO:0048731 system development 41%  GO:0048870 cell motility 41%  GO:0051674 localization of cell 41%  GO:0060326 cell chemotaxis 41%  GO:0060333 interferon-gamma-mediated signaling pathway 38%  GO:0002455 humoral immune response mediated by circulating immunoglobulin 38%  GO:0002495 antigen processing and presentation of peptide antigen via MHC class II 38%  GO:0002685 regulation of leukocyte migration 38%  GO:0009612 response to mechanical stimulus 38%  GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II 38%  GO:0030595 leukocyte chemotaxis 38%  GO:0040012 regulation of locomotion 38%  GO:0050920 regulation of chemotaxis 38%  GO:0051272 positive regulation of cellular component movement 38%  GO:0072358 cardiovascular system development 38%  GO:0072359 circulatory system development 38%  GO:0072376 protein activation cascade 38%  GO:2000145 regulation of cell motility 35%  GO:0001775 cell activation 35%  GO:0007399 nervous system development 35%  GO:0030155 regulation of cell adhesion 35%  GO:0030335 positive regulation of cell migration 35%  GO:0031960 response to corticosteroid stimulus 35%  GO:0048468 cell development 35%  GO:0048583 regulation of response to stimulus 35%  GO:0051239 regulation of multicellular organismal process 35%  GO:0051270 regulation of cellular component movement 35%  GO:2000147 positive regulation of cell motility 32%  GO:0001525 angiogenesis 32%  GO:0002764 immune response-regulating signaling pathway 32%  GO:0007275 multicellular organismal development 32%  GO:0009653 anatomical structure morphogenesis 32%  GO:0014075 response to amine stimulus 32%  GO:0042742 defense response to bacterium 32%  GO:0048514 blood vessel morphogenesis 32%  GO:0048584 positive regulation of response to stimulus 32%  GO:0048856 anatomical structure development 32%  GO:0050793 regulation of developmental process 32%  GO:0050921 positive regulation of chemotaxis 32%  GO:0051384 response to glucocorticoid stimulus 32%  GO:0055093 response to hyperoxia 32%  GO:0070482 response to oxygen levels 29%  GO:0000904 cell morphogenesis involved in differentiation 29%  GO:0002544 chronic inflammatory response 29%  GO:0002688 regulation of leukocyte chemotaxis 29%  GO:0002757 immune response-activating signal transduction 29%  GO:0007162 negative regulation of cell adhesion 29%  GO:0019221 cytokine-mediated signaling pathway 29%  GO:0031099 regeneration 29%  GO:0031294 lymphocyte costimulation 29%  GO:0031295 T cell costimulation 29%  GO:0042063 gliogenesis 29%  GO:0050870 positive regulation of T cell activation 29%  GO:0071222 cellular response to lipopolysaccharide 29%  GO:0071229 cellular response to acid 29%  GO:2000026 regulation of multicellular organismal development 26%  GO:0002768 immune response-regulating cell surface receptor signaling pathway 26%  GO:0006909 phagocytosis 26%  GO:0010035 response to inorganic substance 26%  GO:0016525 negative regulation of angiogenesis 26%  GO:0022008 neurogenesis 26%  GO:0030168 platelet activation 26%  GO:0030182 neuron differentiation 26%  GO:0031175 neuron projection development 26%  GO:0032103 positive regulation of response to external stimulus 26%  GO:0032940 secretion by cell 26%  GO:0032964 collagen biosynthetic process 26%  GO:0042127 regulation of cell proliferation 26%  GO:0048812 neuron projection morphogenesis 26%  GO:0051704 multi-organism process 26%  GO:0065008 regulation of biological quality 26%  GO:0070887 cellular response to chemical stimulus 26%  GO:0071216 cellular response to biotic stimulus 26%  GO:0071219 cellular response to molecule of bacterial origin 26%  GO:0071345 cellular response to cytokine stimulus 24%  GO:0002429 immune response-activating cell surface receptor signaling pathway 24%  GO:0002687 positive regulation of leukocyte migration 24%  GO:0007568 aging 24%  GO:0007596 blood coagulation 24%  GO:0007599 hemostasis 24%  GO:0008360 regulation of cell shape 24%  GO:0014070 response to organic cyclic compound 24%  GO:0030593 neutrophil chemotaxis 24%  GO:0032502 developmental process 24%  GO:0033628 regulation of cell adhesion mediated by integrin 24%  GO:0045766 positive regulation of angiogenesis 24%  GO:0048545 response to steroid hormone stimulus 24%  GO:0048585 negative regulation of response to stimulus 24%  GO:0048666 neuron development 24%  GO:0048667 cell morphogenesis involved in neuron differentiation 24%  GO:0050730 regulation of peptidyl-tyrosine phosphorylation 24%  GO:0050817 coagulation 24%  GO:0050865 regulation of cell activation 24%  GO:0050867 positive regulation of cell activation 24%  GO:0071230 cellular response to amino acid stimulus 21%  GO:0000302 response to reactive oxygen species 21%  GO:0001666 response to hypoxia 21%  GO:0001817 regulation of cytokine production 21%  GO:0002274 myeloid leukocyte activation 21%  GO:0002690 positive regulation of leukocyte chemotaxis 21%  GO:0002694 regulation of leukocyte activation 21%  GO:0007409 axonogenesis 21%  GO:0009719 response to endogenous stimulus 21%  GO:0009888 tissue development 21%  GO:0018149 peptide cross-linking 21%  GO:0030030 cell projection organization 21%  GO:0032570 response to progesterone stimulus 21%  GO:0032989 cellular component morphogenesis 21%  GO:0048660 regulation of smooth muscle cell proliferation 21%  GO:0048699 generation of neurons 21%  GO:0048771 tissue remodeling 21%  GO:0048858 cell projection morphogenesis 21%  GO:0050727 regulation of inflammatory response 21%  GO:0050732 negative regulation of peptidyl-tyrosine phosphorylation 21%  GO:0050795 regulation of behavior 21%  GO:0050851 antigen receptor-mediated signaling pathway 21%  GO:0050863 regulation of T cell activation 21%  GO:0051094 positive regulation of developmental process 21%  GO:0051249 regulation of lymphocyte activation 21%  GO:0051251 positive regulation of lymphocyte activation 21%  GO:0060337 type I interferon-mediated signaling pathway 21%  GO:0071357 cellular response to type I interferon 18%  GO:0000902 cell morphogenesis 18%  GO:0001501 skeletal system development 18%  GO:0002696 positive regulation of leukocyte activation 18%  GO:0006887 exocytosis 18%  GO:0010038 response to metal ion 18%  GO:0010574 regulation of vascular endothelial growth factor production 18%  GO:0019228 regulation of action potential in neuron 18%  GO:0030154 cell differentiation 18%  GO:0032501 multicellular organismal process 18%  GO:0032963 collagen metabolic process 18%  GO:0032990 cell part morphogenesis 18%  GO:0034340 response to type I interferon 18%  GO:0045059 positive thymic T cell selection 18%  GO:0045730 respiratory burst 18%  GO:0048513 organ development 18%  GO:0048520 positive regulation of behavior 18%  GO:0050878 regulation of body fluid levels 18%  GO:0051128 regulation of cellular component organization 18%  GO:0061041 regulation of wound healing 18%  GO:0070372 regulation of ERK1 and ERK2 cascade 18%  GO:0071418 cellular response to amine stimulus 15%  GO:0001503 ossification 15%  GO:0002683 negative regulation of immune system process 15%  GO:0006879 cellular iron ion homeostasis 15%  GO:0006957 complement activation, alternative pathway 15%  GO:0008284 positive regulation of cell proliferation 15%  GO:0010466 negative regulation of peptidase activity 15%  GO:0016337 cell-cell adhesion 15%  GO:0042493 response to drug 15%  GO:0045321 leukocyte activation 15%  GO:0046903 secretion 15%  GO:0048646 anatomical structure formation involved in morphogenesis 15%  GO:0048869 cellular developmental process 15%  GO:0050852 T cell receptor signaling pathway 15%  GO:0050896 response to stimulus 15%  GO:0055072 iron ion homeostasis 15%  GO:0060548 negative regulation of cell death 15%  GO:0071310 cellular response to organic substance 15%  GO:0071675 regulation of mononuclear cell migration 15%  GO:2000097 regulation of smooth muscle cell-matrix adhesion 12%  GO:0001819 positive regulation of cytokine production 12%  GO:0001936 regulation of endothelial cell proliferation 12%  GO:0002697 regulation of immune effector process 12%  GO:0007159 leukocyte cell-cell adhesion 12%  GO:0007229 integrin-mediated signaling pathway 12%  GO:0007417 central nervous system development 12%  GO:0008285 negative regulation of cell proliferation 12%  GO:0009628 response to abiotic stimulus 12%  GO:0010951 negative regulation of endopeptidase activity 12%  GO:0019882 antigen processing and presentation 12%  GO:0030097 hemopoiesis 12%  GO:0030193 regulation of blood coagulation 12%  GO:0031100 organ regeneration 12%  GO:0031102 neuron projection regeneration 12%  GO:0035767 endothelial cell chemotaxis 12%  GO:0042542 response to hydrogen peroxide 12%  GO:0043542 endothelial cell migration 12%  GO:0044259 multicellular organismal macromolecule metabolic process 12%  GO:0045582 positive regulation of T cell differentiation 12%  GO:0050678 regulation of epithelial cell proliferation 12%  GO:0050764 regulation of phagocytosis 12%  GO:0050804 regulation of synaptic transmission 12%  GO:0050853 B cell receptor signaling pathway 12%  GO:0051093 negative regulation of developmental process 12%  GO:0052547 regulation of peptidase activity 12%  GO:0055082 cellular chemical homeostasis 12%  GO:0071417 cellular response to organic nitrogen 12%  GO:0090022 regulation of neutrophil chemotaxis 12%  GO:1900046 regulation of hemostasis 9% GO:0001505 regulation of neurotransmitter levels 9% GO:0001933 negative regulation of protein phosphorylation 9% GO:0002275 myeloid cell activation involved in immune response 9% GO:0002520 immune system development 9% GO:0002699 positive regulation of immune effector process 9% GO:0002886 regulation of myeloid leukocyte mediated immunity 9% GO:0002920 regulation of humoral immune response 9% GO:0003013 circulatory system process 9% GO:0006836 neurotransmitter transport 9% GO:0006873 cellular ion homeostasis 9% GO:0006875 cellular metal ion homeostasis 9% GO:0006897 endocytosis 9% GO:0007267 cell-cell signaling 9% GO:0007268 synaptic transmission 9% GO:0007272 ensheathment of neurons 9% GO:0008015 blood circulation 9% GO:0008366 axon ensheathment 9% GO:0009887 organ morphogenesis 9% GO:0009968 negative regulation of signal transduction 9% GO:0009991 response to extracellular stimulus 9% GO:0010001 glial cell differentiation 9% GO:0010324 membrane invagination 9% GO:0010332 response to gamma radiation 9% GO:0010543 regulation of platelet activation 9% GO:0010646 regulation of cell communication 9% GO:0010648 negative regulation of cell communication 9% GO:0010758 regulation of macrophage chemotaxis 9% GO:0010759 positive regulation of macrophage chemotaxis 9% GO:0010810 regulation of cell-substrate adhesion 9% GO:0010812 negative regulation of cell-substrate adhesion 9% GO:0014910 regulation of smooth muscle cell migration 9% GO:0019226 transmission of nerve impulse 9% GO:0019800 peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan 9% GO:0021529 spinal cord oligodendrocyte cell differentiation 9% GO:0021530 spinal cord oligodendrocyte cell fate specification 9% GO:0023051 regulation of signaling 9% GO:0023057 negative regulation of signaling 9% GO:0030003 cellular cation homeostasis 9% GO:0030098 lymphocyte differentiation 9% GO:0030323 respiratory tube development 9% GO:0030324 lung development 9% GO:0031644 regulation of neurological system process 9% GO:0031663 lipopolysaccharide-mediated signaling pathway 9% GO:0032835 glomerulus development 9% GO:0032944 regulation of mononuclear cell proliferation 9% GO:0035637 multicellular organismal signaling 9% GO:0042102 positive regulation of T cell proliferation 9% GO:0043066 negative regulation of apoptotic process 9% GO:0043069 negative regulation of programmed cell death 9% GO:0043368 positive T cell selection 9% GO:0044057 regulation of system process 9% GO:0044087 regulation of cellular component biogenesis 9% GO:0044236 multicellular organismal metabolic process 9% GO:0045058 T cell selection 9% GO:0045597 positive regulation of cell differentiation 9% GO:0045621 positive regulation of lymphocyte differentiation 9% GO:0046635 positive regulation of alpha-beta T cell activation 9% GO:0048534 hemopoietic or lymphoid organ development 9% GO:0050670 regulation of lymphocyte proliferation 9% GO:0050729 positive regulation of inflammatory response 9% GO:0051240 positive regulation of multicellular organismal process 9% GO:0051969 regulation of transmission of nerve impulse 9% GO:0055001 muscle cell development 9% GO:0055002 striated muscle cell development 9% GO:0055065 metal ion homeostasis 9% GO:0070098 chemokine-mediated signaling pathway 9% GO:0070208 protein heterotrimerization 9% GO:0070663 regulation of leukocyte proliferation 9% GO:0071622 regulation of granulocyte chemotaxis 9% GO:0071901 negative regulation of protein serine/threonine kinase activity 9% GO:0090090 negative regulation of canonical Wnt receptor signaling pathway 6% GO:0000041 transition metal ion transport 6% GO:0000188 inactivation of MAPK activity 6% GO:0001504 neurotransmitter uptake 6% GO:0001508 regulation of action potential 6% GO:0001763 morphogenesis of a branching structure 6% GO:0001776 leukocyte homeostasis 6% GO:0001782 B cell homeostasis 6% GO:0001953 negative regulation of cell-matrix adhesion 6% GO:0002260 lymphocyte homeostasis 6% GO:0002521 leukocyte differentiation 6% GO:0002686 negative regulation of leukocyte migration 6% GO:0002698 negative regulation of immune effector process 6% GO:0002819 regulation of adaptive immune response 6% GO:0002821 positive regulation of adaptive immune response 6% GO:0002822 regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 6% GO:0002824 positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 6% GO:0003008 system process 6% GO:0003094 glomerular filtration 6% GO:0006469 negative regulation of protein kinase activity 6% GO:0006911 phagocytosis, engulfment 6% GO:0006916 anti-apoptosis 6% GO:0007269 neurotransmitter secretion 6% GO:0007411 axon guidance 6% GO:0007566 embryo implantation 6% GO:0009266 response to temperature stimulus 6% GO:0009306 protein secretion 6% GO:0009615 response to virus 6% GO:0009725 response to hormone stimulus 6% GO:0009743 response to carbohydrate stimulus 6% GO:0009966 regulation of signal transduction 6% GO:0010575 positive regulation vascular endothelial growth factor production 6% GO:0010594 regulation of endothelial cell migration 6% GO:0010769 regulation of cell morphogenesis involved in differentiation 6% GO:0010955 negative regulation of protein processing 6% GO:0014052 regulation of gamma-aminobutyric acid secretion 6% GO:0014706 striated muscle tissue development 6% GO:0014805 smooth muscle adaptation 6% GO:0014829 vascular smooth muscle contraction 6% GO:0019725 cellular homeostasis 6% GO:0021545 cranial nerve development 6% GO:0021781 glial cell fate commitment 6% GO:0022604 regulation of cell morphogenesis 6% GO:0022904 respiratory electron transport chain 6% GO:0030029 actin filament-based process 6% GO:0030111 regulation of Wnt receptor signaling pathway 6% GO:0030178 negative regulation of Wnt receptor signaling pathway 6% GO:0030217 T cell differentiation 6% GO:0030224 monocyte differentiation 6% GO:0031347 regulation of defense response 6% GO:0031348 negative regulation of defense response 6% GO:0031349 positive regulation of defense response 6% GO:0031579 membrane raft organization 6% GO:0031589 cell-substrate adhesion 6% GO:0031646 positive regulation of neurological system process 6% GO:0031915 positive regulation of synaptic plasticity 6% GO:0032102 negative regulation of response to external stimulus 6% GO:0032355 response to estradiol stimulus 6% GO:0032642 regulation of chemokine production 6% GO:0032760 positive regulation of tumor necrosis factor production 6% GO:0033003 regulation of mast cell activation 6% GO:0033006 regulation of mast cell activation involved in immune response 6% GO:0033673 negative regulation of kinase activity 6% GO:0034059 response to anoxia 6% GO:0034614 cellular response to reactive oxygen species 6% GO:0035457 cellular response to interferon-alpha 6% GO:0040007 growth 6% GO:0042129 regulation of T cell proliferation 6% GO:0042246 tissue regeneration 6% GO:0042326 negative regulation of phosphorylation 6% GO:0042327 positive regulation of phosphorylation 6% GO:0042552 myelination 6% GO:0042592 homeostatic process 6% GO:0042692 muscle cell differentiation 6% GO:0043304 regulation of mast cell degranulation 6% GO:0043407 negative regulation of MAP kinase activity 6% GO:0043408 regulation of MAPK cascade 6% GO:0043409 negative regulation of MAPK cascade 6% GO:0043627 response to estrogen stimulus 6% GO:0045123 cellular extravasation 6% GO:0045333 cellular respiration 6% GO:0045576 mast cell activation 6% GO:0045586 regulation of gamma-delta T cell differentiation 6% GO:0045588 positive regulation of gamma-delta T cell differentiation 6% GO:0045664 regulation of neuron differentiation 6% GO:0045906 negative regulation of vasoconstriction 6% GO:0046649 lymphocyte activation 6% GO:0048010 vascular endothelial growth factor receptor signaling pathway 6% GO:0048167 regulation of synaptic plasticity 6% GO:0048247 lymphocyte chemotaxis 6% GO:0048286 lung alveolus development 6% GO:0048661 positive regulation of smooth muscle cell proliferation 6% GO:0048709 oligodendrocyte differentiation 6% GO:0048747 muscle fiber development 6% GO:0048872 homeostasis of number of cells 6% GO:0048878 chemical homeostasis 6% GO:0050654 chondroitin sulfate proteoglycan metabolic process 6% GO:0050679 positive regulation of epithelial cell proliferation 6% GO:0050777 negative regulation of immune response 6% GO:0050801 ion homeostasis 6% GO:0050818 regulation of coagulation 6% GO:0050864 regulation of B cell activation 6% GO:0050877 neurological system process 6% GO:0051146 striated muscle cell differentiation 6% GO:0051216 cartilage development 6% GO:0051346 negative regulation of hydrolase activity 6% GO:0051348 negative regulation of transferase activity 6% GO:0051591 response to cAMP 6% GO:0051592 response to calcium ion 6% GO:0051971 positive regulation of transmission of nerve impulse 6% GO:0055006 cardiac cell development 6% GO:0055013 cardiac muscle cell development 6% GO:0055080 cation homeostasis 6% GO:0060056 mammary gland involution 6% GO:0060071 Wnt receptor signaling pathway, planar cell polarity pathway 6% GO:0060284 regulation of cell development 6% GO:0060348 bone development 6% GO:0060537 muscle tissue development 6% GO:0060541 respiratory system development 6% GO:0070374 positive regulation of ERK1 and ERK2 cascade 6% GO:0070665 positive regulation of leukocyte proliferation 6% GO:0072012 glomerulus vasculature development 6% GO:0080134 regulation of response to stress 6% GO:0090175 regulation of establishment of planar polarity 6% GO:0097066 response to thyroid hormone stimulus 6% GO:0097067 cellular response to thyroid hormone stimulus 6% GO:0097205 renal filtration 6% GO:2000377 regulation of reactive oxygen species metabolic process 3% GO:0000272 polysaccharide catabolic process 3% GO:0001300 chronological cell aging 3% GO:0001523 retinoid metabolic process 3% GO:0001562 response to protozoan 3% GO:0001569 patterning of blood vessels 3% GO:0001570 vasculogenesis 3% GO:0001649 osteoblast differentiation 3% GO:0001656 metanephros development 3% GO:0001706 endoderm formation 3% GO:0001754 eye photoreceptor cell differentiation 3% GO:0001766 membrane raft polarization 3% GO:0001774 microglial cell activation 3% GO:0001816 cytokine production 3% GO:0001822 kidney development 3% GO:0001838 embryonic epithelial tube formation 3% GO:0001843 neural tube closure 3% GO:0001878 response to yeast 3% GO:0001894 tissue homeostasis 3% GO:0001938 positive regulation of endothelial cell proliferation 3% GO:0001957 intramembranous ossification 3% GO:0001974 blood vessel remodeling 3% GO:0002009 morphogenesis of an epithelium 3% GO:0002062 chondrocyte differentiation 3% GO:0002064 epithelial cell development 3% GO:0002138 retinoic acid biosynthetic process 3% GO:0002218 activation of innate immune response 3% GO:0002238 response to molecule of fungal origin 3% GO:0002263 cell activation involved in immune response 3% GO:0002279 mast cell activation involved in immune response 3% GO:0002281 macrophage activation involved in immune response 3% GO:0002282 microglial cell activation involved in immune response 3% GO:0002283 neutrophil activation involved in immune response 3% GO:0002366 leukocyte activation involved in immune response 3% GO:0002431 Fc receptor mediated stimulatory signaling pathway 3% GO:0002444 myeloid leukocyte mediated immunity 3% GO:0002448 mast cell mediated immunity 3% GO:0002478 antigen processing and presentation of exogenous peptide antigen 3% GO:0002507 tolerance induction 3% GO:0002526 acute inflammatory response 3% GO:0002532 production of molecular mediator involved in inflammatory response 3% GO:0002543 activation of blood coagulation via clotting cascade 3% GO:0002577 regulation of antigen processing and presentation 3% GO:0002634 regulation of germinal center formation 3% GO:0002673 regulation of acute inflammatory response 3% GO:0002675 positive regulation of acute inflammatory response 3% GO:0002679 respiratory burst involved in defense response 3% GO:0002689 negative regulation of leukocyte chemotaxis 3% GO:0002700 regulation of production of molecular mediator of immune response 3% GO:0002703 regulation of leukocyte mediated immunity 3% GO:0002705 positive regulation of leukocyte mediated immunity 3% GO:0002708 positive regulation of lymphocyte mediated immunity 3% GO:0002820 negative regulation of adaptive immune response 3% GO:0003007 heart morphogenesis 3% GO:0003009 skeletal muscle contraction 3% GO:0003012 muscle system process 3% GO:0003073 regulation of systemic arterial blood pressure 3% GO:0003081 regulation of systemic arterial blood pressure by renin-angiotensin 3% GO:0003158 endothelium development 3% GO:0003205 cardiac chamber development 3% GO:0003206 cardiac chamber morphogenesis 3% GO:0003208 cardiac ventricle morphogenesis 3% GO:0003231 cardiac ventricle development 3% GO:0003382 epithelial cell morphogenesis 3% GO:0005976 polysaccharide metabolic process 3% GO:0006006 glucose metabolic process 3% GO:0006022 aminoglycan metabolic process 3% GO:0006029 proteoglycan metabolic process 3% GO:0006090 pyruvate metabolic process 3% GO:0006096 glycolysis 3% GO:0006120 mitochondrial electron transport, NADH to ubiquinone 3% GO:0006599 phosphagen metabolic process 3% GO:0006600 creatine metabolic process 3% GO:0006633 fatty acid biosynthetic process 3% GO:0006690 icosanoid metabolic process 3% GO:0006720 isoprenoid metabolic process 3% GO:0006790 sulfur compound metabolic process 3% GO:0006826 iron ion transport 3% GO:0006910 phagocytosis, recognition 3% GO:0006929 substrate-dependent cell migration 3% GO:0006936 muscle contraction 3% GO:0006937 regulation of muscle contraction 3% GO:0006941 striated muscle contraction 3% GO:0006968 cellular defense response 3% GO:0006979 response to oxidative stress 3% GO:0007026 negative regulation of microtubule depolymerization 3% GO:0007132 meiotic metaphase I 3% GO:0007154 cell communication 3% GO:0007157 heterophilic cell-cell adhesion 3% GO:0007160 cell-matrix adhesion 3% GO:0007165 signal transduction 3% GO:0007166 cell surface receptor signaling pathway 3% GO:0007199 G-protein signaling, coupled to cGMP nucleotide second messenger 3% GO:0007263 nitric oxide mediated signal transduction 3% GO:0007422 peripheral nervous system development 3% GO:0007507 heart development 3% GO:0007517 muscle organ development 3% GO:0007519 skeletal muscle tissue development 3% GO:0007584 response to nutrient 3% GO:0007589 body fluid secretion 3% GO:0007610 behavior 3% GO:0007611 learning or memory 3% GO:0007612 learning 3% GO:0008217 regulation of blood pressure 3% GO:0008277 regulation of G-protein coupled receptor protein signaling pathway 3% GO:0008283 cell proliferation 3% GO:0008347 glial cell migration 3% GO:0009620 response to fungus 3% GO:0009746 response to hexose stimulus 3% GO:0009756 carbohydrate mediated signaling 3% GO:0010172 embryonic body morphogenesis 3% GO:0010212 response to ionizing radiation 3% GO:0010447 response to acidity 3% GO:0010561 negative regulation of glycoprotein biosynthetic process 3% GO:0010563 negative regulation of phosphorus metabolic process 3% GO:0010595 positive regulation of endothelial cell migration 3% GO:0010740 positive regulation of intracellular protein kinase cascade 3% GO:0010811 positive regulation of cell-substrate adhesion 3% GO:0010927 cellular component assembly involved in morphogenesis 3% GO:0010939 regulation of necrotic cell death 3% GO:0010975 regulation of neuron projection development 3% GO:0014003 oligodendrocyte development 3% GO:0014013 regulation of gliogenesis 3% GO:0014020 primary neural tube formation 3% GO:0014047 glutamate secretion 3% GO:0014068 positive regulation of phosphatidylinositol 3-kinase cascade 3% GO:0014820 tonic smooth muscle contraction 3% GO:0015682 ferric iron transport 3% GO:0016049 cell growth 3% GO:0016101 diterpenoid metabolic process 3% GO:0016331 morphogenesis of embryonic epithelium 3% GO:0016339 calcium-dependent cell-cell adhesion 3% GO:0018108 peptidyl-tyrosine phosphorylation 3% GO:0018212 peptidyl-tyrosine modification 3% GO:0019220 regulation of phosphate metabolic process 3% GO:0019229 regulation of vasoconstriction 3% GO:0019302 D-ribose biosynthetic process 3% GO:0019693 ribose phosphate metabolic process 3% GO:0019827 stem cell maintenance 3% GO:0019884 antigen processing and presentation of exogenous antigen 3% GO:0021542 dentate gyrus development 3% GO:0021602 cranial nerve morphogenesis 3% GO:0021675 nerve development 3% GO:0021782 glial cell development 3% GO:0022614 membrane to membrane docking 3% GO:0022900 electron transport chain 3% GO:0023052 signaling 3% GO:0030036 actin cytoskeleton organization 3% GO:0030048 actin filament-based movement 3% GO:0030049 muscle filament sliding 3% GO:0030194 positive regulation of blood coagulation 3% GO:0030204 chondroitin sulfate metabolic process 3% GO:0030225 macrophage differentiation 3% GO:0030239 myofibril assembly 3% GO:0030240 skeletal muscle thin filament assembly 3% GO:0030278 regulation of ossification 3% GO:0030336 negative regulation of cell migration 3% GO:0030855 epithelial cell differentiation 3% GO:0031032 actomyosin structure organization 3% GO:0031112 positive regulation of microtubule polymerization or depolymerization 3% GO:0031113 regulation of microtubule polymerization 3% GO:0031116 positive regulation of microtubule polymerization 3% GO:0031344 regulation of cell projection organization 3% GO:0031345 negative regulation of cell projection organization 3% GO:0031394 positive regulation of prostaglandin biosynthetic process 3% GO:0031580 membrane raft distribution 3% GO:0031664 regulation of lipopolysaccharide-mediated signaling pathway 3% GO:0031667 response to nutrient levels 3% GO:0032649 regulation of interferon-gamma production 3% GO:0032675 regulation of interleukin-6 production 3% GO:0032677 regulation of interleukin-8 production 3% GO:0032879 regulation of localization 3% GO:0032928 regulation of superoxide anion generation 3% GO:0032930 positive regulation of superoxide anion generation 3% GO:0032946 positive regulation of mononuclear cell proliferation 3% GO:0032956 regulation of actin cytoskeleton organization 3% GO:0032970 regulation of actin filament-based process 3% GO:0033275 actin-myosin filament sliding 3% GO:0033572 transferrin transport 3% GO:0033630 positive regulation of cell adhesion mediated by integrin 3% GO:0033993 response to lipid 3% GO:0034121 regulation of toll-like receptor signaling pathway 3% GO:0034136 negative regulation of toll-like receptor 2 signaling pathway 3% GO:0034284 response to monosaccharide stimulus 3% GO:0034329 cell junction assembly 3% GO:0034330 cell junction organization 3% GO:0034612 response to tumor necrosis factor 3% GO:0034637 cellular carbohydrate biosynthetic process 3% GO:0034755 iron ion transmembrane transport 3% GO:0035148 tube formation 3% GO:0035239 tube morphogenesis 3% GO:0035295 tube development 3% GO:0035385 Roundabout signaling pathway 3% GO:0035583 sequestering of TGFbeta in extracellular matrix 3% GO:0035860 glial cell-derived neurotrophic factor receptor signaling pathway 3% GO:0035924 cellular response to vascular endothelial growth factor stimulus 3% GO:0036072 direct ossification 3% GO:0040013 negative regulation of locomotion 3% GO:0042035 regulation of cytokine biosynthetic process 3% GO:0042108 positive regulation of cytokine biosynthetic process 3% GO:0042110 T cell activation 3% GO:0042116 macrophage activation 3% GO:0042384 cilium assembly 3% GO:0042391 regulation of membrane potential 3% GO:0042730 fibrinolysis 3% GO:0042743 hydrogen peroxide metabolic process 3% GO:0042832 defense response to protozoan 3% GO:0043092 L-amino acid import 3% GO:0043270 positive regulation of ion transport 3% GO:0043277 apoptotic cell clearance 3% GO:0043279 response to alkaloid 3% GO:0043299 leukocyte degranulation 3% GO:0043303 mast cell degranulation 3% GO:0043383 negative T cell selection 3% GO:0043405 regulation of MAP kinase activity 3% GO:0043410 positive regulation of MAPK cascade 3% GO:0043535 regulation of blood vessel endothelial cell migration 3% GO:0043536 positive regulation of blood vessel endothelial cell migration 3% GO:0043549 regulation of kinase activity 3% GO:0044319 wound healing, spreading of cells 3% GO:0045055 regulated secretory pathway 3% GO:0045060 negative thymic T cell selection 3% GO:0045061 thymic T cell selection 3% GO:0045088 regulation of innate immune response 3% GO:0045089 positive regulation of innate immune response 3% GO:0045446 endothelial cell differentiation 3% GO:0045595 regulation of cell differentiation 3% GO:0045596 negative regulation of cell differentiation 3% GO:0045619 regulation of lymphocyte differentiation 3% GO:0045638 negative regulation of myeloid cell differentiation 3% GO:0045667 regulation of osteoblast differentiation 3% GO:0045785 positive regulation of cell adhesion 3% GO:0045859 regulation of protein kinase activity 3% GO:0045923 positive regulation of fatty acid metabolic process 3% GO:0045936 negative regulation of phosphate metabolic process 3% GO:0046364 monosaccharide biosynthetic process 3% GO:0046390 ribose phosphate biosynthetic process 3% GO:0046456 icosanoid biosynthetic process 3% GO:0046530 photoreceptor cell differentiation 3% GO:0046634 regulation of alpha-beta T cell activation 3% GO:0046643 regulation of gamma-delta T cell activation 3% GO:0046645 positive regulation of gamma-delta T cell activation 3% GO:0048002 antigen processing and presentation of peptide antigen 3% GO:0048168 regulation of neuronal synaptic plasticity 3% GO:0048488 synaptic vesicle endocytosis 3% GO:0048489 synaptic vesicle transport 3% GO:0048518 positive regulation of biological process 3% GO:0048519 negative regulation of biological process 3% GO:0048522 positive regulation of cellular process 3% GO:0048589 developmental growth 3% GO:0048638 regulation of developmental growth 3% GO:0048644 muscle organ morphogenesis 3% GO:0048662 negative regulation of smooth muscle cell proliferation 3% GO:0048678 response to axon injury 3% GO:0048704 embryonic skeletal system morphogenesis 3% GO:0048705 skeletal system morphogenesis 3% GO:0048729 tissue morphogenesis 3% GO:0048738 cardiac muscle tissue development 3% GO:0048754 branching morphogenesis of a tube 3% GO:0050663 cytokine secretion 3% GO:0050671 positive regulation of lymphocyte proliferation 3% GO:0050680 negative regulation of epithelial cell proliferation 3% GO:0050728 negative regulation of inflammatory response 3% GO:0050766 positive regulation of phagocytosis 3% GO:0050767 regulation of neurogenesis 3% GO:0050770 regulation of axonogenesis 3% GO:0050806 positive regulation of synaptic transmission 3% GO:0050808 synapse organization 3% GO:0050830 defense response to Gram-positive bacterium 3% GO:0050854 regulation of antigen receptor-mediated signaling pathway 3% GO:0050866 negative regulation of cell activation 3% GO:0050890 cognition 3% GO:0050922 negative regulation of chemotaxis 3% GO:0050926 regulation of positive chemotaxis 3% GO:0051055 negative regulation of lipid biosynthetic process 3% GO:0051129 negative regulation of cellular component organization 3% GO:0051130 positive regulation of cellular component organization 3% GO:0051174 regulation of phosphorus metabolic process 3% GO:0051241 negative regulation of multicellular organismal process 3% GO:0051271 negative regulation of cellular component movement 3% GO:0051305 chromosome movement towards spindle pole 3% GO:0051338 regulation of transferase activity 3% GO:0051387 negative regulation of nerve growth factor receptor signaling pathway 3% GO:0051547 regulation of keratinocyte migration 3% GO:0051549 positive regulation of keratinocyte migration 3% GO:0051593 response to folic acid 3% GO:0051607 defense response to virus 3% GO:0051665 membrane raft localization 3% GO:0051716 cellular response to stimulus 3% GO:0051895 negative regulation of focal adhesion assembly 3% GO:0051896 regulation of protein kinase B signaling cascade 3% GO:0051897 positive regulation of protein kinase B signaling cascade 3% GO:0051917 regulation of fibrinolysis 3% GO:0051928 positive regulation of calcium ion transport 3% GO:0051960 regulation of nervous system development 3% GO:0055003 cardiac myofibril assembly 3% GO:0055007 cardiac muscle cell differentiation 3% GO:0055008 cardiac muscle tissue morphogenesis 3% GO:0060137 maternal process involved in parturition 3% GO:0060231 mesenchymal to epithelial transition 3% GO:0060236 regulation of mitotic spindle organization 3% GO:0060271 cilium morphogenesis 3% GO:0060349 bone morphogenesis 3% GO:0060415 muscle tissue morphogenesis 3% GO:0060420 regulation of heart growth 3% GO:0060426 lung vasculature development 3% GO:0060429 epithelium development 3% GO:0060441 epithelial tube branching involved in lung morphogenesis 3% GO:0060485 mesenchyme development 3% GO:0060538 skeletal muscle organ development 3% GO:0060547 negative regulation of necrotic cell death 3% GO:0060560 developmental growth involved in morphogenesis 3% GO:0060562 epithelial tube morphogenesis 3% GO:0060606 tube closure 3% GO:0060666 dichotomous subdivision of terminal units involved in salivary gland branching 3% GO:0060741 prostate gland stromal morphogenesis 3% GO:0061061 muscle structure development 3% GO:0061138 morphogenesis of a branching epithelium 3% GO:0061318 renal filtration cell differentiation 3% GO:0070168 negative regulation of biomineral tissue development 3% GO:0070201 regulation of establishment of protein localization 3% GO:0070206 protein trimerization 3% GO:0070252 actin-mediated cell contraction 3% GO:0070301 cellular response to hydrogen peroxide 3% GO:0070391 response to lipoteichoic acid 3% GO:0070486 leukocyte aggregation 3% GO:0070507 regulation of microtubule cytoskeleton organization 3% GO:0071214 cellular response to abiotic stimulus 3% GO:0071223 cellular response to lipoteichoic acid 3% GO:0071241 cellular response to inorganic substance 3% GO:0071260 cellular response to mechanical stimulus 3% GO:0071277 cellular response to calcium ion 3% GO:0071322 cellular response to carbohydrate stimulus 3% GO:0071347 cellular response to interleukin-1 3% GO:0071356 cellular response to tumor necrosis factor 3% GO:0071402 cellular response to lipoprotein particle stimulus 3% GO:0071453 cellular response to oxygen levels 3% GO:0071456 cellular response to hypoxia 3% GO:0071671 regulation of smooth muscle cell chemotaxis 3% GO:0071780 mitotic cell cycle G2/M transition checkpoint 3% GO:0071900 regulation of protein serine/threonine kinase activity 3% GO:0072001 renal system development 3% GO:0072006 nephron development 3% GO:0072010 glomerular epithelium development 3% GO:0072015 glomerular visceral epithelial cell development 3% GO:0072102 glomerulus morphogenesis 3% GO:0072109 glomerular mesangium development 3% GO:0072112 glomerular visceral epithelial cell differentiation 3% GO:0072175 epithelial tube formation 3% GO:0072310 glomerular epithelial cell development 3% GO:0072311 glomerular epithelial cell differentiation 3% GO:0090023 positive regulation of neutrophil chemotaxis 3% GO:0090025 regulation of monocyte chemotaxis 3% GO:0090026 positive regulation of monocyte chemotaxis 3% GO:0090050 positive regulation of cell migration involved in sprouting angiogenesis 3% GO:0090092 regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 3% GO:0090257 regulation of muscle system process 3% GO:0097006 regulation of plasma lipoprotein particle levels 3% GO:1900048 positive regulation of hemostasis 3% GO:2000052 positive regulation of non-canonical Wnt receptor signaling pathway 3% GO:2000098 negative regulation of smooth muscle cell-matrix adhesion 3% GO:2000146 negative regulation of cell motility 3% GO:2000177 regulation of neural precursor cell proliferation 3% GO:2000402 negative regulation of lymphocyte migration 3% GO:2001280 positive regulation of unsaturated fatty acid biosynthetic process CLAS (32 Samples) 53%  GO:0007399 nervous system development 38%  GO:0007155 cell adhesion 38%  GO:0022610 biological adhesion 38%  GO:0048731 system development 38%  GO:0071230 cellular response to amino acid stimulus 34%  GO:0001944 vasculature development 34%  GO:0022008 neurogenesis 34%  GO:0030198 extracellular matrix organization 34%  GO:0043062 extracellular structure organization 31%  GO:0001568 blood vessel development 31%  GO:0009611 response to wounding 31%  GO:0030182 neuron differentiation 31%  GO:0048514 blood vessel morphogenesis 31%  GO:0048666 neuron development 31%  GO:0048699 generation of neurons 31%  GO:0048856 anatomical structure development 31%  GO:0071346 cellular response to interferon-gamma 28%  GO:0000904 cell morphogenesis involved in differentiation 28%  GO:0006952 defense response 28%  GO:0007275 multicellular organismal development 28%  GO:0009607 response to biotic stimulus 28%  GO:0009653 anatomical structure morphogenesis 28%  GO:0010033 response to organic substance 28%  GO:0030334 regulation of cell migration 28%  GO:0031175 neuron projection development 28%  GO:0032502 developmental process 28%  GO:0034340 response to type I interferon 28%  GO:0034341 response to interferon-gamma 28%  GO:0040012 regulation of locomotion 28%  GO:0048667 cell morphogenesis involved in neuron differentiation 28%  GO:0048812 neuron projection morphogenesis 28%  GO:0060333 interferon-gamma-mediated signaling pathway 28%  GO:0060337 type I interferon-mediated signaling pathway 28%  GO:0071229 cellular response to acid 28%  GO:0071357 cellular response to type I interferon 28%  GO:0072358 cardiovascular system development 28%  GO:0072359 circulatory system development 28%  GO:2000145 regulation of cell motility 25%  GO:0000902 cell morphogenesis 25%  GO:0007409 axonogenesis 25%  GO:0019221 cytokine-mediated signaling pathway 25%  GO:0030154 cell differentiation 25%  GO:0032989 cellular component morphogenesis 25%  GO:0032990 cell part morphogenesis 25%  GO:0034097 response to cytokine stimulus 25%  GO:0040011 locomotion 25%  GO:0045765 regulation of angiogenesis 25%  GO:0048468 cell development 25%  GO:0048858 cell projection morphogenesis 25%  GO:0048869 cellular developmental process 25%  GO:0051270 regulation of cellular component movement 25%  GO:0051707 response to other organism 25%  GO:0055093 response to hyperoxia 22%  GO:0001101 response to acid 22%  GO:0002376 immune system process 22%  GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 22%  GO:0009605 response to external stimulus 22%  GO:0009615 response to virus 22%  GO:0010243 response to organic nitrogen 22%  GO:0016477 cell migration 22%  GO:0030030 cell projection organization 22%  GO:0042221 response to chemical stimulus 22%  GO:0043200 response to amino acid stimulus 22%  GO:0048545 response to steroid hormone stimulus 22%  GO:0050900 leukocyte migration 22%  GO:0070482 response to oxygen levels 22%  GO:0071345 cellular response to cytokine stimulus 22%  GO:0071417 cellular response to organic nitrogen 22%  GO:0071418 cellular response to amine stimulus 22%  GO:2000147 positive regulation of cell motility 19%  GO:0006935 chemotaxis 19%  GO:0006955 immune response 19%  GO:0007596 blood coagulation 19%  GO:0007599 hemostasis 19%  GO:0009612 response to mechanical stimulus 19%  GO:0009888 tissue development 19%  GO:0030199 collagen fibril organization 19%  GO:0030335 positive regulation of cell migration 19%  GO:0040017 positive regulation of locomotion 19%  GO:0042060 wound healing 19%  GO:0042330 taxis 19%  GO:0050817 coagulation 19%  GO:0050878 regulation of body fluid levels 19%  GO:0051272 positive regulation of cellular component movement 16%  GO:0001525 angiogenesis 16%  GO:0001822 kidney development 16%  GO:0002237 response to molecule of bacterial origin 16%  GO:0006950 response to stress 16%  GO:0006954 inflammatory response 16%  GO:0007272 ensheathment of neurons 16%  GO:0007417 central nervous system development 16%  GO:0007568 aging 16%  GO:0008366 axon ensheathment 16%  GO:0030155 regulation of cell adhesion 16%  GO:0030168 platelet activation 16%  GO:0032355 response to estradiol stimulus 16%  GO:0032496 response to lipopolysaccharide 16%  GO:0042063 gliogenesis 16%  GO:0042552 myelination 16%  GO:0045087 innate immune response 16%  GO:0050793 regulation of developmental process 16%  GO:0070887 cellular response to chemical stimulus 16%  GO:0071310 cellular response to organic substance 13%  GO:0001666 response to hypoxia 13%  GO:0001775 cell activation 13%  GO:0002495 antigen processing and presentation of peptide antigen via MHC class II 13%  GO:0003008 system process 13%  GO:0006928 cellular component movement 13%  GO:0007162 negative regulation of cell adhesion 13%  GO:0010035 response to inorganic substance 13%  GO:0014075 response to amine stimulus 13%  GO:0016064 immunoglobulin mediated immune response 13%  GO:0019228 regulation of action potential in neuron 13%  GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II 13%  GO:0022603 regulation of anatomical structure morphogenesis 13%  GO:0032101 regulation of response to external stimulus 13%  GO:0032570 response to progesterone stimulus 13%  GO:0043627 response to estrogen stimulus 13%  GO:0048583 regulation of response to stimulus 13%  GO:0048584 positive regulation of response to stimulus 13%  GO:0048870 cell motility 13%  GO:0051239 regulation of multicellular organismal process 13%  GO:0051674 localization of cell 13%  GO:0051704 multi-organism process 13%  GO:0060326 cell chemotaxis 13%  GO:0060541 respiratory system development 13%  GO:2000026 regulation of multicellular organismal development 9% GO:0001505 regulation of neurotransmitter levels 9% GO:0001508 regulation of action potential 9% GO:0002250 adaptive immune response 9% GO:0002252 immune effector process 9% GO:0002253 activation of immune response 9% GO:0002443 leukocyte mediated immunity 9% GO:0002449 lymphocyte mediated immunity 9% GO:0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 9% GO:0002576 platelet degranulation 9% GO:0002682 regulation of immune system process 9% GO:0002684 positive regulation of immune system process 9% GO:0002768 immune response-regulating cell surface receptor signaling pathway 9% GO:0006836 neurotransmitter transport 9% GO:0006959 humoral immune response 9% GO:0007267 cell-cell signaling 9% GO:0007268 synaptic transmission 9% GO:0007269 neurotransmitter secretion 9% GO:0007411 axon guidance 9% GO:0008347 glial cell migration 9% GO:0009266 response to temperature stimulus 9% GO:0009617 response to bacterium 9% GO:0009719 response to endogenous stimulus 9% GO:0014003 oligodendrocyte development 9% GO:0014013 regulation of gliogenesis 9% GO:0014047 glutamate secretion 9% GO:0014910 regulation of smooth muscle cell migration 9% GO:0016525 negative regulation of angiogenesis 9% GO:0019226 transmission of nerve impulse 9% GO:0019724 B cell mediated immunity 9% GO:0030593 neutrophil chemotaxis 9% GO:0031099 regeneration 9% GO:0032501 multicellular organismal process 9% GO:0032835 glomerulus development 9% GO:0032879 regulation of localization 9% GO:0032964 collagen biosynthetic process 9% GO:0035637 multicellular organismal signaling 9% GO:0042391 regulation of membrane potential 9% GO:0042493 response to drug 9% GO:0044259 multicellular organismal macromolecule metabolic process 9% GO:0045428 regulation of nitric oxide biosynthetic process 9% GO:0045766 positive regulation of angiogenesis 9% GO:0048488 synaptic vesicle endocytosis 9% GO:0048489 synaptic vesicle transport 9% GO:0048513 organ development 9% GO:0048585 negative regulation of response to stimulus 9% GO:0048709 oligodendrocyte differentiation 9% GO:0050730 regulation of peptidyl-tyrosine phosphorylation 9% GO:0050776 regulation of immune response 9% GO:0050778 positive regulation of immune response 9% GO:0050804 regulation of synaptic transmission 9% GO:0050865 regulation of cell activation 9% GO:0050877 neurological system process 9% GO:0050920 regulation of chemotaxis 9% GO:0051969 regulation of transmission of nerve impulse 9% GO:0055082 cellular chemical homeostasis 9% GO:0060236 regulation of mitotic spindle organization 9% GO:0070208 protein heterotrimerization 9% GO:0071219 cellular response to molecule of bacterial origin 9% GO:0071222 cellular response to lipopolysaccharide 9% GO:0072001 renal system development 9% GO:0072012 glomerulus vasculature development 9% GO:0072239 metanephric glomerulus vasculature development 6% GO:0000075 cell cycle checkpoint 6% GO:0000087 M phase of mitotic cell cycle 6% GO:0000236 mitotic prometaphase 6% GO:0000278 mitotic cell cycle 6% GO:0000279 M phase 6% GO:0000280 nuclear division 6% GO:0000302 response to reactive oxygen species 6% GO:0001501 skeletal system development 6% GO:0001504 neurotransmitter uptake 6% GO:0001817 regulation of cytokine production 6% GO:0002429 immune response-activating cell surface receptor signaling pathway 6% GO:0002455 humoral immune response mediated by circulating immunoglobulin 6% GO:0002520 immune system development 6% GO:0002521 leukocyte differentiation 6% GO:0002544 chronic inflammatory response 6% GO:0002675 positive regulation of acute inflammatory response 6% GO:0002683 negative regulation of immune system process 6% GO:0002685 regulation of leukocyte migration 6% GO:0002690 positive regulation of leukocyte chemotaxis 6% GO:0002694 regulation of leukocyte activation 6% GO:0003001 generation of a signal involved in cell-cell signaling 6% GO:0006260 DNA replication 6% GO:0006693 prostaglandin metabolic process 6% GO:0006873 cellular ion homeostasis 6% GO:0006909 phagocytosis 6% GO:0006916 anti-apoptosis 6% GO:0006956 complement activation 6% GO:0006958 complement activation, classical pathway 6% GO:0007067 mitosis 6% GO:0007160 cell-matrix adhesion 6% GO:0007166 cell surface receptor signaling pathway 6% GO:0007416 synapse assembly 6% GO:0008284 positive regulation of cell proliferation 6% GO:0008285 negative regulation of cell proliferation 6% GO:0009628 response to abiotic stimulus 6% GO:0009887 organ morphogenesis 6% GO:0010001 glial cell differentiation 6% GO:0010564 regulation of cell cycle process 6% GO:0010646 regulation of cell communication 6% GO:0010647 positive regulation of cell communication 6% GO:0010812 negative regulation of cell-substrate adhesion 6% GO:0014014 negative regulation of gliogenesis 6% GO:0014070 response to organic cyclic compound 6% GO:0016337 cell-cell adhesion 6% GO:0019229 regulation of vasoconstriction 6% GO:0019882 antigen processing and presentation 6% GO:0022402 cell cycle process 6% GO:0022403 cell cycle phase 6% GO:0023051 regulation of signaling 6% GO:0023052 signaling 6% GO:0023056 positive regulation of signaling 6% GO:0023061 signal release 6% GO:0030097 hemopoiesis 6% GO:0030098 lymphocyte differentiation 6% GO:0030595 leukocyte chemotaxis 6% GO:0031102 neuron projection regeneration 6% GO:0031294 lymphocyte costimulation 6% GO:0031295 T cell costimulation 6% GO:0031589 cell-substrate adhesion 6% GO:0031644 regulation of neurological system process 6% GO:0031663 lipopolysaccharide-mediated signaling pathway 6% GO:0031960 response to corticosteroid stimulus 6% GO:0032103 positive regulation of response to external stimulus 6% GO:0032940 secretion by cell 6% GO:0035295 tube development 6% GO:0035457 cellular response to interferon-alpha 6% GO:0035924 cellular response to vascular endothelial growth factor stimulus 6% GO:0042127 regulation of cell proliferation 6% GO:0042476 odontogenesis 6% GO:0043086 negative regulation of catalytic activity 6% GO:0044057 regulation of system process 6% GO:0044236 multicellular organismal metabolic process 6% GO:0045321 leukocyte activation 6% GO:0045429 positive regulation of nitric oxide biosynthetic process 6% GO:0046903 secretion 6% GO:0048010 vascular endothelial growth factor receptor signaling pathway 6% GO:0048167 regulation of synaptic plasticity 6% GO:0048285 organelle fission 6% GO:0048519 negative regulation of biological process 6% GO:0048520 positive regulation of behavior 6% GO:0048706 embryonic skeletal system development 6% GO:0050727 regulation of inflammatory response 6% GO:0050729 positive regulation of inflammatory response 6% GO:0050732 negative regulation of peptidyl-tyrosine phosphorylation 6% GO:0050795 regulation of behavior 6% GO:0050808 synapse organization 6% GO:0050851 antigen receptor-mediated signaling pathway 6% GO:0050867 positive regulation of cell activation 6% GO:0050870 positive regulation of T cell activation 6% GO:0050896 response to stimulus 6% GO:0050921 positive regulation of chemotaxis 6% GO:0051050 positive regulation of transport 6% GO:0051384 response to glucocorticoid stimulus 6% GO:0052547 regulation of peptidase activity 6% GO:0060627 regulation of vesicle-mediated transport 6% GO:0061041 regulation of wound healing 6% GO:0061298 retina vasculature development in camera-type eye 6% GO:0070372 regulation of ERK1 and ERK2 cascade 6% GO:0071156 regulation of cell cycle arrest 6% GO:0071216 cellular response to biotic stimulus 6% GO:0072006 nephron development 6% GO:0072224 metanephric glomerulus development 6% GO:0072376 protein activation cascade 6% GO:0080134 regulation of response to stress 6% GO:2000097 regulation of smooth muscle cell-matrix adhesion 3% GO:0000070 mitotic sister chromatid segregation 3% GO:0000082 G1/S transition of mitotic cell cycle 3% GO:0000226 microtubule cytoskeleton organization 3% GO:0000819 sister chromatid segregation 3% GO:0001655 urogenital system development 3% GO:0001656 metanephros development 3% GO:0001736 establishment of planar polarity 3% GO:0001796 regulation of type Ila hypersensitivity 3% GO:0001798 positive regulation of type Ila hypersensitivity 3% GO:0001889 liver development 3% GO:0001893 maternal placenta development 3% GO:0001915 negative regulation of T cell mediated cytotoxicity 3% GO:0001933 negative regulation of protein phosphorylation 3% GO:0002011 morphogenesis of an epithelial sheet 3% GO:0002138 retinoic acid biosynthetic process 3% GO:0002175 protein localization to paranode region of axon 3% GO:0002246 wound healing involved in inflammatory response 3% GO:0002274 myeloid leukocyte activation 3% GO:0002474 antigen processing and presentation of peptide antigen via MHC class I 3% GO:0002478 antigen processing and presentation of exogenous peptide antigen 3% GO:0002479 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent 3% GO:0002480 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent 3% GO:0002507 tolerance induction 3% GO:0002526 acute inflammatory response 3% GO:0002673 regulation of acute inflammatory response 3% GO:0002687 positive regulation of leukocyte migration 3% GO:0002688 regulation of leukocyte chemotaxis 3% GO:0002697 regulation of immune effector process 3% GO:0002698 negative regulation of immune effector process 3% GO:0002699 positive regulation of immune effector process 3% GO:0002703 regulation of leukocyte mediated immunity 3% GO:0002706 regulation of lymphocyte mediated immunity 3% GO:0002709 regulation of T cell mediated immunity 3% GO:0002718 regulation of cytokine production involved in immune response 3% GO:0002757 immune response-activating signal transduction 3% GO:0002764 immune response-regulating signaling pathway 3% GO:0002765 immune response-inhibiting signal transduction 3% GO:0002767 immune response-inhibiting cell surface receptor signaling pathway 3% GO:0002774 Fc receptor mediated inhibitory signaling pathway 3% GO:0002819 regulation of adaptive immune response 3% GO:0002820 negative regulation of adaptive immune response 3% GO:0002822 regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 3% GO:0002888 positive regulation of myeloid leukocyte mediated immunity 3% GO:0002889 regulation of immunoglobulin mediated immune response 3% GO:0002892 regulation of type II hypersensitivity 3% GO:0002894 positive regulation of type II hypersensitivity 3% GO:0003002 regionalization 3% GO:0003013 circulatory system process 3% GO:0003094 glomerular filtration 3% GO:0003149 membranous septum morphogenesis 3% GO:0003150 muscular septum morphogenesis 3% GO:0003281 ventricular septum development 3% GO:0006259 DNA metabolic process 3% GO:0006261 DNA-dependent DNA replication 3% GO:0006270 DNA-dependent DNA replication initiation 3% GO:0006271 DNA strand elongation involved in DNA replication 3% GO:0006281 DNA repair 3% GO:0006323 DNA packaging 3% GO:0006333 chromatin assembly or disassembly 3% GO:0006334 nucleosome assembly 3% GO:0006336 DNA replication-independent nucleosome assembly 3% GO:0006692 prostanoid metabolic process 3% GO:0006811 ion transport 3% GO:0006812 cation transport 3% GO:0006814 sodium ion transport 3% GO:0006821 chloride transport 3% GO:0006826 iron ion transport 3% GO:0006879 cellular iron ion homeostasis 3% GO:0006887 exocytosis 3% GO:0006996 organelle organization 3% GO:0007010 cytoskeleton organization 3% GO:0007017 microtubule-based process 3% GO:0007018 microtubule-based movement 3% GO:0007049 cell cycle 3% GO:0007051 spindle organization 3% GO:0007059 chromosome segregation 3% GO:0007076 mitotic chromosome condensation 3% GO:0007093 mitotic cell cycle checkpoint 3% GO:0007094 mitotic cell cycle spindle assembly checkpoint 3% GO:0007156 homophilic cell adhesion 3% GO:0007159 leukocyte cell-cell adhesion 3% GO:0007164 establishment of tissue polarity 3% GO:0007165 signal transduction 3% GO:0007179 transforming growth factor beta receptor signaling pathway 3% GO:0007194 negative regulation of adenylate cyclase activity 3% GO:0007199 G-protein signaling, coupled to cGMP nucleotide second messenger 3% GO:0007214 gamma-aminobutyric acid signaling pathway 3% GO:0007229 integrin-mediated signaling pathway 3% GO:0007346 regulation of mitotic cell cycle 3% GO:0007420 brain development 3% GO:0007431 salivary gland development 3% GO:0007517 muscle organ development 3% GO:0007610 behavior 3% GO:0007611 learning or memory 3% GO:0007612 learning 3% GO:0007613 memory 3% GO:0008015 blood circulation 3% GO:0008217 regulation of blood pressure 3% GO:0008360 regulation of cell shape 3% GO:0008406 gonad development 3% GO:0009221 pyrimidine deoxyribonucleotide biosynthetic process 3% GO:0009263 deoxyribonucleotide biosynthetic process 3% GO:0009306 protein secretion 3% GO:0009725 response to hormone stimulus 3% GO:0009743 response to carbohydrate stimulus 3% GO:0009746 response to hexose stimulus 3% GO:0009749 response to glucose stimulus 3% GO:0009792 embryo development ending in birth or egg hatching 3% GO:0009952 anterior/posterior pattern specification 3% GO:0009954 proximal/distal pattern formation 3% GO:0009967 positive regulation of signal transduction 3% GO:0010038 response to metal ion 3% GO:0010332 response to gamma radiation 3% GO:0010466 negative regulation of peptidase activity 3% GO:0010563 negative regulation of phosphorus metabolic process 3% GO:0010574 regulation of vascular endothelial growth factor production 3% GO:0010648 negative regulation of cell communication 3% GO:0010716 negative regulation of extracellular matrix disassembly 3% GO:0010718 positive regulation of epithelial to mesenchymal transition 3% GO:0010720 positive regulation of cell development 3% GO:0010721 negative regulation of cell development 3% GO:0010758 regulation of macrophage chemotaxis 3% GO:0010759 positive regulation of macrophage chemotaxis 3% GO:0010810 regulation of cell-substrate adhesion 3% GO:0010811 positive regulation of cell-substrate adhesion 3% GO:0010935 regulation of macrophage cytokine production 3% GO:0010936 negative regulation of macrophage cytokine production 3% GO:0010941 regulation of cell death 3% GO:0010951 negative regulation of endopeptidase activity 3% GO:0010955 negative regulation of protein processing 3% GO:0014015 positive regulation of gliogenesis 3% GO:0014706 striated muscle tissue development 3% GO:0014805 smooth muscle adaptation 3% GO:0015672 monovalent inorganic cation transport 3% GO:0015698 inorganic anion transport 3% GO:0015807 L-amino acid transport 3% GO:0016043 cellular component organization 3% GO:0016048 detection of temperature stimulus 3% GO:0016079 synaptic vesicle exocytosis 3% GO:0016188 synaptic vesicle maturation 3% GO:0016339 calcium-dependent cell-cell adhesion 3% GO:0018149 peptide cross-linking 3% GO:0019725 cellular homeostasis 3% GO:0019884 antigen processing and presentation of exogenous antigen 3% GO:0021529 spinal cord oligodendrocyte cell differentiation 3% GO:0021530 spinal cord oligodendrocyte cell fate specification 3% GO:0021537 telencephalon development 3% GO:0021543 pallium development 3% GO:0021778 oligodendrocyte cell fate specification 3% GO:0021780 glial cell fate specification 3% GO:0021782 glial cell development 3% GO:0021882 regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment 3% GO:0021893 cerebral cortex GABAergic interneuron fate commitment 3% GO:0021953 central nervous system neuron differentiation 3% GO:0021954 central nervous system neuron development 3% GO:0022010 central nervous system myelination 3% GO:0022406 membrane docking 3% GO:0022409 positive regulation of cell-cell adhesion 3% GO:0022602 ovulation cycle process 3% GO:0022604 regulation of cell morphogenesis 3% GO:0022614 membrane to membrane docking 3% GO:0022616 DNA strand elongation 3% GO:0023057 negative regulation of signaling 3% GO:0030001 metal ion transport 3% GO:0030036 actin cytoskeleton organization 3% GO:0030071 regulation of mitotic metaphase/anaphase transition 3% GO:0030100 regulation of endocytosis 3% GO:0030111 regulation of Wnt receptor signaling pathway 3% GO:0030217 T cell differentiation 3% GO:0030261 chromosome condensation 3% GO:0030323 respiratory tube development 3% GO:0030324 lung development 3% GO:0030800 negative regulation of cyclic nucleotide metabolic process 3% GO:0030803 negative regulation of cyclic nucleotide biosynthetic process 3% GO:0030809 negative regulation of nucleotide biosynthetic process 3% GO:0030815 negative regulation of cAMP metabolic process 3% GO:0030818 negative regulation of cAMP biosynthetic process 3% GO:0031055 chromatin remodeling at centromere 3% GO:0031100 organ regeneration 3% GO:0031280 negative regulation of cyclase activity 3% GO:0031344 regulation of cell projection organization 3% GO:0031347 regulation of defense response 3% GO:0031497 chromatin assembly 3% GO:0031577 spindle checkpoint 3% GO:0031646 positive regulation of neurological system process 3% GO:0032091 negative regulation of protein binding 3% GO:0032228 regulation of synaptic transmission, GABAergic 3% GO:0032291 axon ensheathment in central nervous system 3% GO:0032680 regulation of tumor necrosis factor production 3% GO:0032763 regulation of mast cell cytokine production 3% GO:0032944 regulation of mononuclear cell proliferation 3% GO:0032963 collagen metabolic process 3% GO:0033003 regulation of mast cell activation 3% GO:0034080 CenH3-containing nucleosome assembly at centromere 3% GO:0034220 ion transmembrane transport 3% GO:0034284 response to monosaccharide stimulus 3% GO:0034447 very-low-density lipoprotein particle clearance 3% GO:0034508 centromere complex assembly 3% GO:0034612 response to tumor necrosis factor 3% GO:0034724 DNA replication-independent nucleosome organization 3% GO:0034728 nucleosome organization 3% GO:0035239 tube morphogenesis 3% GO:0035567 non-canonical Wnt receptor signaling pathway 3% GO:0035850 epithelial cell differentiation involved in kidney development 3% GO:0042129 regulation of T cell proliferation 3% GO:0042312 regulation of vasodilation 3% GO:0042326 negative regulation of phosphorylation 3% GO:0042554 superoxide anion generation 3% GO:0042590 antigen processing and presentation of exogenous peptide antigen via MHC class I 3% GO:0042592 homeostatic process 3% GO:0042742 defense response to bacterium 3% GO:0042981 regulation of apoptotic process 3% GO:0043009 chordate embryonic development 3% GO:0043044 ATP-dependent chromatin remodeling 3% GO:0043066 negative regulation of apoptotic process 3% GO:0043069 negative regulation of programmed cell death 3% GO:0043092 L-amino acid import 3% GO:0043299 leukocyte degranulation 3% GO:0043368 positive T cell selection 3% GO:0043393 regulation of protein binding 3% GO:0043405 regulation of MAP kinase activity 3% GO:0043408 regulation of MAPK cascade 3% GO:0043486 histone exchange 3% GO:0043550 regulation of lipid kinase activity 3% GO:0043552 positive regulation of phosphatidylinositol 3-kinase activity 3% GO:0043584 nose development 3% GO:0043588 skin development 3% GO:0044092 negative regulation of molecular function 3% GO:0044246 regulation of multicellular organismal metabolic process 3% GO:0045058 T cell selection 3% GO:0045059 positive thymic T cell selection 3% GO:0045061 thymic T cell selection 3% GO:0045137 development of primary sexual characteristics 3% GO:0045596 negative regulation of cell differentiation 3% GO:0045664 regulation of neuron differentiation 3% GO:0045665 negative regulation of neuron differentiation 3% GO:0045685 regulation of glial cell differentiation 3% GO:0045686 negative regulation of glial cell differentiation 3% GO:0045787 positive regulation of cell cycle 3% GO:0045839 negative regulation of mitosis 3% GO:0045841 negative regulation of mitotic metaphase/anaphase transition 3% GO:0045907 positive regulation of vasoconstriction 3% GO:0045909 positive regulation of vasodilation 3% GO:0045936 negative regulation of phosphate metabolic process 3% GO:0045980 negative regulation of nucleotide metabolic process 3% GO:0046697 decidualization 3% GO:0048002 antigen processing and presentation of peptide antigen 3% GO:0048008 platelet-derived growth factor receptor signaling pathway 3% GO:0048168 regulation of neuronal synaptic plasticity 3% GO:0048523 negative regulation of cellular process 3% GO:0048534 hemopoietic or lymphoid organ development 3% GO:0048568 embryonic organ development 3% GO:0048608 reproductive structure development 3% GO:0048646 anatomical structure formation involved in morphogenesis 3% GO:0048660 regulation of smooth muscle cell proliferation 3% GO:0048661 positive regulation of smooth muscle cell proliferation 3% GO:0048663 neuron fate commitment 3% GO:0048676 axon extension involved in development 3% GO:0048678 response to axon injury 3% GO:0048704 embryonic skeletal system morphogenesis 3% GO:0048705 skeletal system morphogenesis 3% GO:0048713 regulation of oligodendrocyte differentiation 3% GO:0048715 negative regulation of oligodendrocyte differentiation 3% GO:0048736 appendage development 3% GO:0048741 skeletal muscle fiber development 3% GO:0048771 tissue remodeling 3% GO:0048872 homeostasis of number of cells 3% GO:0048878 chemical homeostasis 3% GO:0050000 chromosome localization 3% GO:0050663 cytokine secretion 3% GO:0050665 hydrogen peroxide biosynthetic process 3% GO:0050670 regulation of lymphocyte proliferation 3% GO:0050767 regulation of neurogenesis 3% GO:0050777 negative regulation of immune response 3% GO:0050801 ion homeostasis 3% GO:0050806 positive regulation of synaptic transmission 3% GO:0050852 T cell receptor signaling pathway 3% GO:0050864 regulation of B cell activation 3% GO:0050890 cognition 3% GO:0050922 negative regulation of chemotaxis 3% GO:0050926 regulation of positive chemotaxis 3% GO:0050927 positive regulation of positive chemotaxis 3% GO:0051049 regulation of transport 3% GO:0051093 negative regulation of developmental process 3% GO:0051094 positive regulation of developmental process 3% GO:0051098 regulation of binding 3% GO:0051100 negative regulation of binding 3% GO:0051128 regulation of cellular component organization 3% GO:0051216 cartilage development 3% GO:0051240 positive regulation of multicellular organismal process 3% GO:0051241 negative regulation of multicellular organismal process 3% GO:0051249 regulation of lymphocyte activation 3% GO:0051276 chromosome organization 3% GO:0051301 cell division 3% GO:0051303 establishment of chromosome localization 3% GO:0051325 interphase 3% GO:0051329 interphase of mitotic cell cycle 3% GO:0051346 negative regulation of hydrolase activity 3% GO:0051350 negative regulation of lyase activity 3% GO:0051383 kinetochore organization 3% GO:0051482 elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger 3% GO:0051668 localization within membrane 3% GO:0051716 cellular response to stimulus 3% GO:0051726 regulation of cell cycle 3% GO:0051782 negative regulation of cell division 3% GO:0051784 negative regulation of nuclear division 3% GO:0051960 regulation of nervous system development 3% GO:0051971 positive regulation of transmission of nerve impulse 3% GO:0051983 regulation of chromosome segregation 3% GO:0055002 striated muscle cell development 3% GO:0055072 iron ion homeostasis 3% GO:0055085 transmembrane transport 3% GO:0060071 Wnt receptor signaling pathway, planar cell polarity pathway 3% GO:0060173 limb development 3% GO:0060348 bone development 3% GO:0060412 ventricular septum morphogenesis 3% GO:0060441 epithelial tube branching involved in lung morphogenesis 3% GO:0060537 muscle tissue development 3% GO:0060548 negative regulation of cell death 3% GO:0060712 spongiotrophoblast layer development 3% GO:0061008 hepaticobiliary system development 3% GO:0061061 muscle structure development 3% GO:0061138 morphogenesis of a branching epithelium 3% GO:0061318 renal filtration cell differentiation 3% GO:0061351 neural precursor cell proliferation 3% GO:0065004 protein-DNA complex assembly 3% GO:0065008 regulation of biological quality 3% GO:0070374 positive regulation of ERK1 and ERK2 cascade 3% GO:0070555 response to interleukin-1 3% GO:0070613 regulation of protein processing 3% GO:0070663 regulation of leukocyte proliferation 3% GO:0070664 negative regulation of leukocyte proliferation 3% GO:0071103 DNA conformation change 3% GO:0071173 spindle assembly checkpoint 3% GO:0071174 mitotic cell cycle spindle checkpoint 3% GO:0071248 cellular response to metal ion 3% GO:0071260 cellular response to mechanical stimulus 3% GO:0071276 cellular response to cadmium ion 3% GO:0071277 cellular response to calcium ion 3% GO:0071347 cellular response to interleukin-1 3% GO:0071356 cellular response to tumor necrosis factor 3% GO:0071455 cellular response to hyperoxia 3% GO:0071637 regulation of monocyte chemotactic protein-1 production 3% GO:0071675 regulation of mononuclear cell migration 3% GO:0071824 protein-DNA complex subunit organization 3% GO:0071840 cellular component organization or biogenesis 3% GO:0071841 cellular component organization or biogenesis at cellular level 3% GO:0071842 cellular component organization at cellular level 3% GO:0072010 glomerular epithelium development 3% GO:0072109 glomerular mesangium development 3% GO:0072110 glomerular mesangial cell proliferation 3% GO:0072112 glomerular visceral epithelial cell differentiation 3% GO:0072311 glomerular epithelial cell differentiation 3% GO:0090025 regulation of monocyte chemotaxis 3% GO:0090049 regulation of cell migration involved in sprouting angiogenesis 3% GO:0090175 regulation of establishment of planar polarity 3% GO:0090224 regulation of spindle organization 3% GO:0097205 renal filtration 3% GO:2000300 regulation of synaptic vesicle exocytosis 3% GO:2000401 regulation of lymphocyte migration 3% GO:2000402 negative regulation of lymphocyte migration 3% GO:2000501 regulation of natural killer cell chemotaxis SL (20 Samples) 80%  GO:0007399 nervous system development 55%  GO:0022008 neurogenesis 50%  GO:0048699 generation of neurons 40%  GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 40%  GO:0042063 gliogenesis 35%  GO:0030182 neuron differentiation 35%  GO:0048468 cell development 30%  GO:0007417 central nervous system development 30%  GO:0048167 regulation of synaptic plasticity 30%  GO:0048731 system development 30%  GO:0048856 anatomical structure development 30%  GO:0050793 regulation of developmental process 25%  GO:0001568 blood vessel development 25%  GO:0010001 glial cell differentiation 25%  GO:0010033 response to organic substance 25%  GO:0031960 response to corticosteroid stimulus 25%  GO:0034341 response to interferon-gamma 25%  GO:0051384 response to glucocorticoid stimulus 25%  GO:0060333 interferon-gamma-mediated signaling pathway 25%  GO:0071229 cellular response to acid 25%  GO:0071346 cellular response to interferon-gamma 20%  GO:0001101 response to acid 20%  GO:0001944 vasculature development 20%  GO:0002495 antigen processing and presentation of peptide antigen via MHC class II 20%  GO:0006952 defense response 20%  GO:0007267 cell-cell signaling 20%  GO:0007268 synaptic transmission 20%  GO:0007269 neurotransmitter secretion 20%  GO:0007275 multicellular organismal development 20%  GO:0010243 response to organic nitrogen 20%  GO:0014013 regulation of gliogenesis 20%  GO:0014047 glutamate secretion 20%  GO:0019226 transmission of nerve impulse 20%  GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II 20%  GO:0031644 regulation of neurological system process 20%  GO:0032940 secretion by cell 20%  GO:0035295 tube development 20%  GO:0035637 multicellular organismal signaling 20%  GO:0048168 regulation of neuronal synaptic plasticity 20%  GO:0048489 synaptic vesicle transport 20%  GO:0048709 oligodendrocyte differentiation 20%  GO:0050767 regulation of neurogenesis 20%  GO:0050804 regulation of synaptic transmission 20%  GO:0050877 neurological system process 20%  GO:0051093 negative regulation of developmental process 20%  GO:0051960 regulation of nervous system development 20%  GO:0051969 regulation of transmission of nerve impulse 20%  GO:2000026 regulation of multicellular organismal development 15%  GO:0000904 cell morphogenesis involved in differentiation 15%  GO:0001505 regulation of neurotransmitter levels 15%  GO:0001822 kidney development 15%  GO:0003001 generation of a signal involved in cell-cell signaling 15%  GO:0003008 system process 15%  GO:0006836 neurotransmitter transport 15%  GO:0007155 cell adhesion 15%  GO:0007409 axonogenesis 15%  GO:0008284 positive regulation of cell proliferation 15%  GO:0009611 response to wounding 15%  GO:0009653 anatomical structure morphogenesis 15%  GO:0016064 immunoglobulin mediated immune response 15%  GO:0019228 regulation of action potential in neuron 15%  GO:0019724 B cell mediated immunity 15%  GO:0022603 regulation of anatomical structure morphogenesis 15%  GO:0022610 biological adhesion 15%  GO:0023061 signal release 15%  GO:0030030 cell projection organization 15%  GO:0030154 cell differentiation 15%  GO:0030323 respiratory tube development 15%  GO:0030324 lung development 15%  GO:0031175 neuron projection development 15%  GO:0034097 response to cytokine stimulus 15%  GO:0035239 tube morphogenesis 15%  GO:0042127 regulation of cell proliferation 15%  GO:0042221 response to chemical stimulus 15%  GO:0043066 negative regulation of apoptotic process 15%  GO:0043069 negative regulation of programmed cell death 15%  GO:0043200 response to amino acid stimulus 15%  GO:0044057 regulation of system process 15%  GO:0045595 regulation of cell differentiation 15%  GO:0045596 negative regulation of cell differentiation 15%  GO:0045915 positive regulation of catecholamine metabolic process 15%  GO:0045964 positive regulation of dopamine metabolic process 15%  GO:0048666 neuron development 15%  GO:0048667 cell morphogenesis involved in neuron differentiation 15%  GO:0048712 negative regulation of astrocyte differentiation 15%  GO:0048812 neuron projection morphogenesis 15%  GO:0048869 cellular developmental process 15%  GO:0050890 cognition 15%  GO:0051239 regulation of multicellular organismal process 15%  GO:0060541 respiratory system development 15%  GO:0072001 renal system development 10%  GO:0000902 cell morphogenesis 10%  GO:0001838 embryonic epithelial tube formation 10%  GO:0002250 adaptive immune response 10%  GO:0002252 immune effector process 10%  GO:0002376 immune system process 10%  GO:0002443 leukocyte mediated immunity 10%  GO:0002449 lymphocyte mediated immunity 10%  GO:0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 10%  GO:0002682 regulation of immune system process 10%  GO:0002684 positive regulation of immune system process 10%  GO:0006887 exocytosis 10%  GO:0006955 immune response 10%  GO:0006956 complement activation 10%  GO:0006959 humoral immune response 10%  GO:0007214 gamma-aminobutyric acid signaling pathway 10%  GO:0007219 Notch signaling pathway 10%  GO:0007272 ensheathment of neurons 10%  GO:0007610 behavior 10%  GO:0007611 learning or memory 10%  GO:0008366 axon ensheathment 10%  GO:0009719 response to endogenous stimulus 10%  GO:0014075 response to amine stimulus 10%  GO:0016477 cell migration 10%  GO:0019221 cytokine-mediated signaling pathway 10%  GO:0019827 stem cell maintenance 10%  GO:0021778 oligodendrocyte cell fate specification 10%  GO:0021780 glial cell fate specification 10%  GO:0021781 glial cell fate commitment 10%  GO:0030168 platelet activation 10%  GO:0030199 collagen fibril organization 10%  GO:0030334 regulation of cell migration 10%  GO:0030595 leukocyte chemotaxis 10%  GO:0032101 regulation of response to external stimulus 10%  GO:0032501 multicellular organismal process 10%  GO:0032989 cellular component morphogenesis 10%  GO:0032990 cell part morphogenesis 10%  GO:0034340 response to type I interferon 10%  GO:0035019 somatic stem cell maintenance 10%  GO:0035148 tube formation 10%  GO:0040011 locomotion 10%  GO:0042391 regulation of membrane potential 10%  GO:0042552 myelination 10%  GO:0045087 innate immune response 10%  GO:0045664 regulation of neuron differentiation 10%  GO:0045665 negative regulation of neuron differentiation 10%  GO:0046903 secretion 10%  GO:0048488 synaptic vesicle endocytosis 10%  GO:0048514 blood vessel morphogenesis 10%  GO:0048545 response to steroid hormone stimulus 10%  GO:0048583 regulation of response to stimulus 10%  GO:0048584 positive regulation of response to stimulus 10%  GO:0048729 tissue morphogenesis 10%  GO:0048858 cell projection morphogenesis 10%  GO:0048864 stem cell development 10%  GO:0048870 cell motility 10%  GO:0050806 positive regulation of synaptic transmission 10%  GO:0050900 leukocyte migration 10%  GO:0050920 regulation of chemotaxis 10%  GO:0051050 positive regulation of transport 10%  GO:0051674 localization of cell 10%  GO:0060284 regulation of cell development 10%  GO:0060326 cell chemotaxis 10%  GO:0060337 type I interferon-mediated signaling pathway 10%  GO:0060548 negative regulation of cell death 10%  GO:0060562 epithelial tube morphogenesis 10%  GO:0060627 regulation of vesicle-mediated transport 10%  GO:0071357 cellular response to type I interferon 10%  GO:0072070 loop of Henle development 10%  GO:0072175 epithelial tube formation 5% GO:0000302 response to reactive oxygen species 5% GO:0001504 neurotransmitter uptake 5% GO:0001655 urogenital system development 5% GO:0001656 metanephros development 5% GO:0001738 morphogenesis of a polarized epithelium 5% GO:0001796 regulation of type IIa hypersensitivity 5% GO:0001798 positive regulation of type IIa hypersensitivity 5% GO:0001843 neural tube closure 5% GO:0002009 morphogenesis of an epithelium 5% GO:0002053 positive regulation of mesenchymal cell proliferation 5% GO:0002237 response to molecule of bacterial origin 5% GO:0002253 activation of immune response 5% GO:0002274 myeloid leukocyte activation 5% GO:0002282 microglial cell activation involved in immune response 5% GO:0002429 immune response-activating cell surface receptor signaling pathway 5% GO:0002431 Fc receptor mediated stimulatory signaling pathway 5% GO:0002455 humoral immune response mediated by circulating immunoglobulin 5% GO:0002507 tolerance induction 5% GO:0002576 platelet degranulation 5% GO:0002685 regulation of leukocyte migration 5% GO:0002687 positive regulation of leukocyte migration 5% GO:0002688 regulation of leukocyte chemotaxis 5% GO:0002690 positive regulation of leukocyte chemotaxis 5% GO:0002694 regulation of leukocyte activation 5% GO:0002696 positive regulation of leukocyte activation 5% GO:0002757 immune response-activating signal transduction 5% GO:0002764 immune response-regulating signaling pathway 5% GO:0002768 immune response-regulating cell surface receptor signaling pathway 5% GO:0002886 regulation of myeloid leukocyte mediated immunity 5% GO:0002888 positive regulation of myeloid leukocyte mediated immunity 5% GO:0002892 regulation of type II hypersensitivity 5% GO:0002894 positive regulation of type II hypersensitivity 5% GO:0003094 glomerular filtration 5% GO:0006119 oxidative phosphorylation 5% GO:0006120 mitochondrial electron transport, NADH to ubiquinone 5% GO:0006821 chloride transport 5% GO:0006928 cellular component movement 5% GO:0006935 chemotaxis 5% GO:0006954 inflammatory response 5% GO:0006958 complement activation, classical pathway 5% GO:0007160 cell-matrix adhesion 5% GO:0007263 nitric oxide mediated signal transduction 5% GO:0007568 aging 5% GO:0007584 response to nutrient 5% GO:0007596 blood coagulation 5% GO:0007599 hemostasis 5% GO:0007612 learning 5% GO:0007626 locomotory behavior 5% GO:0008347 glial cell migration 5% GO:0009124 nucleoside monophosphate biosynthetic process 5% GO:0009605 response to external stimulus 5% GO:0009612 response to mechanical stimulus 5% GO:0009888 tissue development 5% GO:0009967 positive regulation of signal transduction 5% GO:0009991 response to extracellular stimulus 5% GO:0010035 response to inorganic substance 5% GO:0010212 response to ionizing radiation 5% GO:0010332 response to gamma radiation 5% GO:0010563 negative regulation of phosphorus metabolic process 5% GO:0010574 regulation of vascular endothelial growth factor production 5% GO:0010575 positive regulation vascular endothelial growth factor production 5% GO:0010621 negative regulation of transcription by transcription factor localization 5% GO:0010646 regulation of cell communication 5% GO:0010647 positive regulation of cell communication 5% GO:0010765 positive regulation of sodium ion transport 5% GO:0010812 negative regulation of cell-substrate adhesion 5% GO:0010873 positive regulation of cholesterol esterification 5% GO:0010935 regulation of macrophage cytokine production 5% GO:0014014 negative regulation of gliogenesis 5% GO:0014015 positive regulation of gliogenesis 5% GO:0014020 primary neural tube formation 5% GO:0014032 neural crest cell development 5% GO:0014033 neural crest cell differentiation 5% GO:0015698 inorganic anion transport 5% GO:0016079 synaptic vesicle exocytosis 5% GO:0016192 vesicle-mediated transport 5% GO:0016331 morphogenesis of embryonic epithelium 5% GO:0016339 calcium-dependent cell-cell adhesion 5% GO:0017156 calcium ion-dependent exocytosis 5% GO:0017157 regulation of exocytosis 5% GO:0021529 spinal cord oligodendrocyte cell differentiation 5% GO:0021530 spinal cord oligodendrocyte cell fate specification 5% GO:0021779 oligodendrocyte cell fate commitment 5% GO:0021915 neural tube development 5% GO:0021952 central nervous system projection neuron axonogenesis 5% GO:0021955 central nervous system neuron axonogenesis 5% GO:0022010 central nervous system myelination 5% GO:0022900 electron transport chain 5% GO:0022904 respiratory electron transport chain 5% GO:0023052 signaling 5% GO:0023056 positive regulation of signaling 5% GO:0030097 hemopoiesis 5% GO:0030155 regulation of cell adhesion 5% GO:0030198 extracellular matrix organization 5% GO:0030335 positive regulation of cell migration 5% GO:0030593 neutrophil chemotaxis 5% GO:0031099 regeneration 5% GO:0031294 lymphocyte costimulation 5% GO:0031295 T cell costimulation 5% GO:0031579 membrane raft organization 5% GO:0031589 cell-substrate adhesion 5% GO:0031646 positive regulation of neurological system process 5% GO:0031667 response to nutrient levels 5% GO:0032103 positive regulation of response to external stimulus 5% GO:0032291 axon ensheathment in central nervous system 5% GO:0032502 developmental process 5% GO:0032879 regulation of localization 5% GO:0032930 positive regulation of superoxide anion generation 5% GO:0033273 response to vitamin 5% GO:0034382 chylomicron remnant clearance 5% GO:0035282 segmentation 5% GO:0035850 epithelial cell differentiation involved in kidney development 5% GO:0040012 regulation of locomotion 5% GO:0040017 positive regulation of locomotion 5% GO:0042326 negative regulation of phosphorylation 5% GO:0042330 taxis 5% GO:0042493 response to drug 5% GO:0042773 ATP synthesis coupled electron transport 5% GO:0042775 mitochondrial ATP synthesis coupled electron transport 5% GO:0043062 extracellular structure organization 5% GO:0043270 positive regulation of ion transport 5% GO:0043299 leukocyte degranulation 5% GO:0045598 regulation of fat cell differentiation 5% GO:0045599 negative regulation of fat cell differentiation 5% GO:0045607 regulation of auditory receptor cell differentiation 5% GO:0045631 regulation of mechanoreceptor differentiation 5% GO:0045685 regulation of glial cell differentiation 5% GO:0045686 negative regulation of glial cell differentiation 5% GO:0045765 regulation of angiogenesis 5% GO:0045767 regulation of anti-apoptosis 5% GO:0045768 positive regulation of anti-apoptosis 5% GO:0045936 negative regulation of phosphate metabolic process 5% GO:0046826 negative regulation of protein export from nucleus 5% GO:0046928 regulation of neurotransmitter secretion 5% GO:0048041 focal adhesion assembly 5% GO:0048146 positive regulation of fibroblast proliferation 5% GO:0048520 positive regulation of behavior 5% GO:0048523 negative regulation of cellular process 5% GO:0048534 hemopoietic or lymphoid organ development 5% GO:0048646 anatomical structure formation involved in morphogenesis 5% GO:0048710 regulation of astrocyte differentiation 5% GO:0048754 branching morphogenesis of a tube 5% GO:0048863 stem cell differentiation 5% GO:0050678 regulation of epithelial cell proliferation 5% GO:0050764 regulation of phagocytosis 5% GO:0050776 regulation of immune response 5% GO:0050778 positive regulation of immune response 5% GO:0050795 regulation of behavior 5% GO:0050817 coagulation 5% GO:0050851 antigen receptor-mediated signaling pathway 5% GO:0050863 regulation of T cell activation 5% GO:0050864 regulation of B cell activation 5% GO:0050865 regulation of cell activation 5% GO:0050866 negative regulation of cell activation 5% GO:0050867 positive regulation of cell activation 5% GO:0050870 positive regulation of T cell activation 5% GO:0050921 positive regulation of chemotaxis 5% GO:0050926 regulation of positive chemotaxis 5% GO:0050927 positive regulation of positive chemotaxis 5% GO:0050930 induction of positive chemotaxis 5% GO:0051049 regulation of transport 5% GO:0051249 regulation of lymphocyte activation 5% GO:0051251 positive regulation of lymphocyte activation 5% GO:0051270 regulation of cellular component movement 5% GO:0051272 positive regulation of cellular component movement 5% GO:0051414 response to cortisol stimulus 5% GO:0051823 regulation of synapse structural plasticity 5% GO:0051899 membrane depolarization 5% GO:0051971 positive regulation of transmission of nerve impulse 5% GO:0052031 modulation by symbiont of host defense response 5% GO:0052173 response to defenses of other organism involved in symbiotic interaction 5% GO:0052200 response to host defenses 5% GO:0052255 modulation by organism of defense response of other organism involved in symbiotic interaction 5% GO:0052509 positive regulation by symbiont of host defense response 5% GO:0052510 positive regulation by organism of defense response of other organism involved in symbiotic interaction 5% GO:0052564 response to immune response of other organism involved in symbiotic interaction 5% GO:0052572 response to host immune response 5% GO:0060079 regulation of excitatory postsynaptic membrane potential 5% GO:0060425 lung morphogenesis 5% GO:0060429 epithelium development 5% GO:0060606 tube closure 5% GO:0060688 regulation of morphogenesis of a branching structure 5% GO:0060696 regulation of phospholipid catabolic process 5% GO:0060697 positive regulation of phospholipid catabolic process 5% GO:0060907 positive regulation of macrophage cytokine production 5% GO:0061041 regulation of wound healing 5% GO:0061081 positive regulation of myeloid leukocyte cytokine production involved in immune response 5% GO:0065008 regulation of biological quality 5% GO:0070482 response to oxygen levels 5% GO:0070887 cellular response to chemical stimulus 5% GO:0071216 cellular response to biotic stimulus 5% GO:0071219 cellular response to molecule of bacterial origin 5% GO:0071222 cellular response to lipopolysaccharide 5% GO:0071230 cellular response to amino acid stimulus 5% GO:0071310 cellular response to organic substance 5% GO:0071345 cellular response to cytokine stimulus 5% GO:0071418 cellular response to amine stimulus 5% GO:0071470 cellular response to osmotic stress 5% GO:0071675 regulation of mononuclear cell migration 5% GO:0071830 triglyceride-rich lipoprotein particle clearance 5% GO:0072006 nephron development 5% GO:0072080 nephron tubule development 5% GO:0072358 cardiovascular system development 5% GO:0072359 circulatory system development 5% GO:0075136 response to host 5% GO:0090072 positive regulation of sodium ion transport via voltage-gated sodium channel activity 5% GO:0090183 regulation of kidney development 5% GO:0097205 renal filtration 5% GO:2000145 regulation of cell motility 5% GO:2000147 positive regulation of cell motility 5% GO:2000980 regulation of inner ear receptor cell differentiation PROLIF (31 Samples) 74%  GO:0000236 mitotic prometaphase 71%  GO:0000087 M phase of mitotic cell cycle 71%  GO:0000278 mitotic cell cycle 71%  GO:0000280 nuclear division 71%  GO:0007067 mitosis 71%  GO:0048285 organelle fission 68%  GO:0007059 chromosome segregation 68%  GO:0022403 cell cycle phase 65%  GO:0000279 M phase 65%  GO:0022402 cell cycle process 61%  GO:0000075 cell cycle checkpoint 61%  GO:0007049 cell cycle 61%  GO:0051301 cell division 58%  GO:0000819 sister chromatid segregation 58%  GO:0010564 regulation of cell cycle process 58%  GO:0071156 regulation of cell cycle arrest 52%  GO:0000070 mitotic sister chromatid segregation 52%  GO:0006323 DNA packaging 52%  GO:0007051 spindle organization 48%  GO:0006260 DNA replication 48%  GO:0006336 DNA replication-independent nucleosome assembly 48%  GO:0031577 spindle checkpoint 48%  GO:0034080 CenH3-containing nucleosome assembly at centromere 48%  GO:0034724 DNA replication-independent nucleosome organization 48%  GO:0071103 DNA conformation change 45%  GO:0031055 chromatin remodeling at centromere 45%  GO:0043486 histone exchange 45%  GO:0051325 interphase 45%  GO:0051329 interphase of mitotic cell cycle 45%  GO:0051726 regulation of cell cycle 42%  GO:0006261 DNA-dependent DNA replication 42%  GO:0006334 nucleosome assembly 42%  GO:0007399 nervous system development 42%  GO:0031497 chromatin assembly 42%  GO:0042063 gliogenesis 42%  GO:0051276 chromosome organization 42%  GO:0065004 protein-DNA complex assembly 39%  GO:0006259 DNA metabolic process 39%  GO:0006271 DNA strand elongation involved in DNA replication 39%  GO:0043044 ATP-dependent chromatin remodeling 39%  GO:0051983 regulation of chromosome segregation 39%  GO:0071824 protein-DNA complex subunit organization 35%  GO:0000226 microtubule cytoskeleton organization 35%  GO:0007417 central nervous system development 35%  GO:0022616 DNA strand elongation 35%  GO:0034728 nucleosome organization 32%  GO:0000082 G1/S transition of mitotic cell cycle 32%  GO:0006333 chromatin assembly or disassembly 32%  GO:0007017 microtubule-based process 32%  GO:0022008 neurogenesis 32%  GO:0030071 regulation of mitotic metaphase/anaphase transition 32%  GO:0048709 oligodendrocyte differentiation 32%  GO:0071174 mitotic cell cycle spindle checkpoint 29%  GO:0007052 mitotic spindle organization 29%  GO:0007093 mitotic cell cycle checkpoint 29%  GO:0010001 glial cell differentiation 29%  GO:0032201 telomere maintenance via semi-conservative replication 29%  GO:0045841 negative regulation of mitotic metaphase/anaphase transition 29%  GO:0048468 cell development 29%  GO:0048699 generation of neurons 26%  GO:0000216 M/G1 transition of mitotic cell cycle 26%  GO:0006270 DNA-dependent DNA replication initiation 26%  GO:0006312 mitotic recombination 26%  GO:0006996 organelle organization 26%  GO:0007076 mitotic chromosome condensation 26%  GO:0007094 mitotic cell cycle spindle assembly checkpoint 26%  GO:0007346 regulation of mitotic cell cycle 26%  GO:0021781 glial cell fate commitment 26%  GO:0045664 regulation of neuron differentiation 26%  GO:0048015 phosphatidylinositol-mediated signaling 26%  GO:0048017 inositol lipid-mediated signaling 26%  GO:0071173 spindle assembly checkpoint 23%  GO:0000084 S phase of mitotic cell cycle 23%  GO:0000722 telomere maintenance via recombination 23%  GO:0001944 vasculature development 23%  GO:0007088 regulation of mitosis 23%  GO:0007155 cell adhesion 23%  GO:0022610 biological adhesion 23%  GO:0030182 neuron differentiation 23%  GO:0045839 negative regulation of mitosis 23%  GO:0048812 neuron projection morphogenesis 23%  GO:0050767 regulation of neurogenesis 23%  GO:0050793 regulation of developmental process 23%  GO:0051093 negative regulation of developmental process 23%  GO:0051320 S phase 23%  GO:0051783 regulation of nuclear division 23%  GO:0051784 negative regulation of nuclear division 19%  GO:0001568 blood vessel development 19%  GO:0006281 DNA repair 19%  GO:0006974 response to DNA damage stimulus 19%  GO:0014013 regulation of gliogenesis 19%  GO:0030198 extracellular matrix organization 19%  GO:0030261 chromosome condensation 19%  GO:0043062 extracellular structure organization 19%  GO:0045665 negative regulation of neuron differentiation 19%  GO:0048731 system development 19%  GO:0051988 regulation of attachment of spindle microtubules to kinetochore 19%  GO:0060284 regulation of cell development 19%  GO:0071842 cellular component organization at cellular level 19%  GO:2000026 regulation of multicellular organismal development 16%  GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 16%  GO:0006297 nucleotide-excision repair, DNA gap filling 16%  GO:0006310 DNA recombination 16%  GO:0006338 chromatin remodeling 16%  GO:0007275 multicellular organismal development 16%  GO:0010833 telomere maintenance via telomere lengthening 16%  GO:0010948 negative regulation of cell cycle process 16%  GO:0030154 cell differentiation 16%  GO:0030199 collagen fibril organization 16%  GO:0031145 anaphase-promoting complex-dependent proteasomal ubiquitin- dependent protein catabolic process 16%  GO:0048666 neuron development 16%  GO:0048856 anatomical structure development 16%  GO:0051383 kinetochore organization 16%  GO:0071841 cellular component organization or biogenesis at cellular level 16%  GO:0072358 cardiovascular system development 16%  GO:0072359 circulatory system development 13%  GO:0000723 telomere maintenance 13%  GO:0000904 cell morphogenesis involved in differentiation 13%  GO:0001101 response to acid 13%  GO:0001501 skeletal system development 13%  GO:0007409 axonogenesis 13%  GO:0009653 anatomical structure morphogenesis 13%  GO:0009887 organ morphogenesis 13%  GO:0014014 negative regulation of gliogenesis 13%  GO:0021529 spinal cord oligodendrocyte cell differentiation 13%  GO:0021530 spinal cord oligodendrocyte cell fate specification 13%  GO:0022603 regulation of anatomical structure morphogenesis 13%  GO:0032200 telomere organization 13%  GO:0034340 response to type I interferon 13%  GO:0034341 response to interferon-gamma 13%  GO:0045595 regulation of cell differentiation 13%  GO:0045685 regulation of glial cell differentiation 13%  GO:0045686 negative regulation of glial cell differentiation 13%  GO:0048514 blood vessel morphogenesis 13%  GO:0048667 cell morphogenesis involved in neuron differentiation 13%  GO:0048713 regulation of oligodendrocyte differentiation 13%  GO:0048858 cell projection morphogenesis 13%  GO:0048869 cellular developmental process 13%  GO:0051960 regulation of nervous system development 13%  GO:0071229 cellular response to acid 13%  GO:0071346 cellular response to interferon-gamma 10%  GO:0000079 regulation of cyclin-dependent protein kinase activity 10%  GO:0000089 mitotic metaphase 10%  GO:0000902 cell morphogenesis 10%  GO:0006415 translational termination 10%  GO:0010389 regulation of G2/M transition of mitotic cell cycle 10%  GO:0016043 cellular component organization 10%  GO:0019080 viral genome expression 10%  GO:0019083 viral transcription 10%  GO:0021782 glial cell development 10%  GO:0030030 cell projection organization 10%  GO:0031175 neuron projection development 10%  GO:0031397 negative regulation of protein ubiquitination 10%  GO:0032989 cellular component morphogenesis 10%  GO:0032990 cell part morphogenesis 10%  GO:0034508 centromere complex assembly 10%  GO:0035295 tube development 10%  GO:0043200 response to amino acid stimulus 10%  GO:0048706 embryonic skeletal system development 10%  GO:0048710 regulation of astrocyte differentiation 10%  GO:0051323 metaphase 10%  GO:0051436 negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle 10%  GO:0060337 type I interferon-mediated signaling pathway 10%  GO:0071230 cellular response to amino acid stimulus 10%  GO:0071276 cellular response to cadmium ion 10%  GO:0071277 cellular response to calcium ion 10%  GO:0071357 cellular response to type I interferon 10%  GO:0071840 cellular component organization or biogenesis 10%  GO:0090068 positive regulation of cell cycle process 6% GO:0000083 regulation of transcription involved in G1/S phase of mitotic cell cycle 6% GO:0000085 G2 phase of mitotic cell cycle 6% GO:0000910 cytokinesis 6% GO:0001656 metanephros development 6% GO:0001838 embryonic epithelial tube formation 6% GO:0002495 antigen processing and presentation of peptide antigen via MHC class II 6% GO:0006302 double-strand break repair 6% GO:0006364 rRNA processing 6% GO:0006412 translation 6% GO:0006414 translational elongation 6% GO:0006928 cellular component movement 6% GO:0006952 defense response 6% GO:0006958 complement activation, classical pathway 6% GO:0007091 mitotic metaphase/anaphase transition 6% GO:0007568 aging 6% GO:0008608 attachment of spindle microtubules to kinetochore 6% GO:0009263 deoxyribonucleotide biosynthetic process 6% GO:0009888 tissue development 6% GO:0010639 negative regulation of organelle organization 6% GO:0010720 positive regulation of cell development 6% GO:0010721 negative regulation of cell development 6% GO:0010812 negative regulation of cell-substrate adhesion 6% GO:0014003 oligodendrocyte development 6% GO:0014015 positive regulation of gliogenesis 6% GO:0016072 rRNA metabolic process 6% GO:0016331 morphogenesis of embryonic epithelium 6% GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II 6% GO:0021778 oligodendrocyte cell fate specification 6% GO:0021780 glial cell fate specification 6% GO:0021953 central nervous system neuron differentiation 6% GO:0022613 ribonucleoprotein complex biogenesis 6% GO:0030111 regulation of Wnt receptor signaling pathway 6% GO:0031102 neuron projection regeneration 6% GO:0031400 negative regulation of protein modification process 6% GO:0031960 response to corticosteroid stimulus 6% GO:0032467 positive regulation of cytokinesis 6% GO:0032502 developmental process 6% GO:0032886 regulation of microtubule-based process 6% GO:0032964 collagen biosynthetic process 6% GO:0033043 regulation of organelle organization 6% GO:0033205 cell cycle cytokinesis 6% GO:0034097 response to cytokine stimulus 6% GO:0034621 cellular macromolecular complex subunit organization 6% GO:0034622 cellular macromolecular complex assembly 6% GO:0035019 somatic stem cell maintenance 6% GO:0035148 tube formation 6% GO:0042127 regulation of cell proliferation 6% GO:0042254 ribosome biogenesis 6% GO:0043624 cellular protein complex disassembly 6% GO:0043933 macromolecular complex subunit organization 6% GO:0044259 multicellular organismal macromolecule metabolic process 6% GO:0045596 negative regulation of cell differentiation 6% GO:0045786 negative regulation of cell cycle 6% GO:0048736 appendage development 6% GO:0048741 skeletal muscle fiber development 6% GO:0048747 muscle fiber development 6% GO:0050000 chromosome localization 6% GO:0050769 positive regulation of neurogenesis 6% GO:0051094 positive regulation of developmental process 6% GO:0051128 regulation of cellular component organization 6% GO:0051129 negative regulation of cellular component organization 6% GO:0051290 protein heterotetramerization 6% GO:0051303 establishment of chromosome localization 6% GO:0051319 G2 phase 6% GO:0051340 regulation of ligase activity 6% GO:0051352 negative regulation of ligase activity 6% GO:0051437 positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle 6% GO:0051438 regulation of ubiquitin-protein ligase activity 6% GO:0051439 regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle 6% GO:0051444 negative regulation of ubiquitin-protein ligase activity 6% GO:0051984 positive regulation of chromosome segregation 6% GO:0055002 striated muscle cell development 6% GO:0055093 response to hyperoxia 6% GO:0060173 limb development 6% GO:0060333 interferon-gamma-mediated signaling pathway 6% GO:0060541 respiratory system development 6% GO:0060564 negative regulation of mitotic anaphase-promoting complex activity 6% GO:0070208 protein heterotrimerization 6% GO:0070507 regulation of microtubule cytoskeleton organization 6% GO:0070777 D-aspartate transport 6% GO:0070779 D-aspartate import 6% GO:0071248 cellular response to metal ion 6% GO:0071775 regulation of cell cycle cytokinesis 6% GO:0071777 positive regulation of cell cycle cytokinesis 6% GO:0072001 renal system development 6% GO:0072006 nephron development 6% GO:0072175 epithelial tube formation 6% GO:0090090 negative regulation of canonical Wnt receptor signaling pathway 6% GO:2000736 regulation of stem cell differentiation 3% GO:0000077 DNA damage checkpoint 3% GO:0000086 G2/M transition of mitotic cell cycle 3% GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 3% GO:0000956 nuclear-transcribed mRNA catabolic process 3% GO:0001503 ossification 3% GO:0001655 urogenital system development 3% GO:0001666 response to hypoxia 3% GO:0001763 morphogenesis of a branching structure 3% GO:0001822 kidney development 3% GO:0001841 neural tube formation 3% GO:0001843 neural tube closure 3% GO:0002455 humoral immune response mediated by circulating immunoglobulin 3% GO:0002480 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent 3% GO:0002544 chronic inflammatory response 3% GO:0002576 platelet degranulation 3% GO:0002685 regulation of leukocyte migration 3% GO:0002687 positive regulation of leukocyte migration 3% GO:0002688 regulation of leukocyte chemotaxis 3% GO:0002690 positive regulation of leukocyte chemotaxis 3% GO:0003002 regionalization 3% GO:0003105 negative regulation of glomerular filtration 3% GO:0003170 heart valve development 3% GO:0003179 heart valve morphogenesis 3% GO:0003207 cardiac chamber formation 3% GO:0003211 cardiac ventricle formation 3% GO:0003281 ventricular septum development 3% GO:0006119 oxidative phosphorylation 3% GO:0006120 mitochondrial electron transport, NADH to ubiquinone 3% GO:0006139 nucleobase-containing compound metabolic process 3% GO:0006221 pyrimidine nucleotide biosynthetic process 3% GO:0006325 chromatin organization 3% GO:0006396 RNA processing 3% GO:0006401 RNA catabolic process 3% GO:0006402 mRNA catabolic process 3% GO:0006413 translational initiation 3% GO:0006563 L-serine metabolic process 3% GO:0006564 L-serine biosynthetic process 3% GO:0006612 protein targeting to membrane 3% GO:0006613 cotranslational protein targeting to membrane 3% GO:0006614 SRP-dependent cotranslational protein targeting to membrane 3% GO:0006807 nitrogen compound metabolic process 3% GO:0006935 chemotaxis 3% GO:0006950 response to stress 3% GO:0006955 immune response 3% GO:0006956 complement activation 3% GO:0007010 cytoskeleton organization 3% GO:0007062 sister chromatid cohesion 3% GO:0007126 meiosis 3% GO:0007127 meiosis 1 3% GO:0007162 negative regulation of cell adhesion 3% GO:0007219 Notch signaling pathway 3% GO:0007263 nitric oxide mediated signal transduction 3% GO:0007272 ensheathment of neurons 3% GO:0007389 pattern specification process 3% GO:0007411 axon guidance 3% GO:0007420 brain development 3% GO:0008283 cell proliferation 3% GO:0008285 negative regulation of cell proliferation 3% GO:0008344 adult locomotory behavior 3% GO:0008347 glial cell migration 3% GO:0008366 axon ensheathment 3% GO:0009059 macromolecule biosynthetic process 3% GO:0009147 pyrimidine nucleoside triphosphate metabolic process 3% GO:0009148 pyrimidine nucleoside triphosphate biosynthetic process 3% GO:0009186 deoxyribonucleoside diphosphate metabolic process 3% GO:0009262 deoxyribonucleotide metabolic process 3% GO:0009605 response to external stimulus 3% GO:0009607 response to biotic stimulus 3% GO:0009611 response to wounding 3% GO:0009612 response to mechanical stimulus 3% GO:0009615 response to virus 3% GO:0009628 response to abiotic stimulus 3% GO:0009954 proximal/distal pattern formation 3% GO:0010033 response to organic substance 3% GO:0010243 response to organic nitrogen 3% GO:0010467 gene expression 3% GO:0010498 proteasomal protein catabolic process 3% GO:0010594 regulation of endothelial cell migration 3% GO:0010718 positive regulation of epithelial to mesenchymal transition 3% GO:0010759 positive regulation of macrophage chemotaxis 3% GO:0010769 regulation of cell morphogenesis involved in differentiation 3% GO:0010770 positive regulation of cell morphogenesis involved in differentiation 3% GO:0010975 regulation of neuron projection development 3% GO:0010977 negative regulation of neuron projection development 3% GO:0014020 primary neural tube formation 3% GO:0014052 regulation of gamma-aminobutyric acid secretion 3% GO:0014054 positive regulation of gamma-aminobutyric acid secretion 3% GO:0014070 response to organic cyclic compound 3% GO:0014075 response to amine stimulus 3% GO:0014706 striated muscle tissue development 3% GO:0014812 muscle cell migration 3% GO:0015949 nucleobase-containing small molecule interconversion 3% GO:0015980 energy derivation by oxidation of organic compounds 3% GO:0016064 immunoglobulin mediated immune response 3% GO:0016070 RNA metabolic process 3% GO:0016071 mRNA metabolic process 3% GO:0016477 cell migration 3% GO:0016525 negative regulation of angiogenesis 3% GO:0018149 peptide cross-linking 3% GO:0019058 viral infectious cycle 3% GO:0019221 cytokine-mediated signaling pathway 3% GO:0019228 regulation of action potential in neuron 3% GO:0019724 B cell mediated immunity 3% GO:0019827 stem cell maintenance 3% GO:0019985 translesion synthesis 3% GO:0021510 spinal cord development 3% GO:0021517 ventral spinal cord development 3% GO:0021522 spinal cord motor neuron differentiation 3% GO:0021542 dentate gyrus development 3% GO:0021779 oligodendrocyte cell fate commitment 3% GO:0021915 neural tube development 3% GO:0022411 cellular component disassembly 3% GO:0022415 viral reproductive process 3% GO:0022604 regulation of cell morphogenesis 3% GO:0022900 electron transport chain 3% GO:0022904 respiratory electron transport chain 3% GO:0030178 negative regulation of Wnt receptor signaling pathway 3% GO:0030204 chondroitin sulfate metabolic process 3% GO:0030278 regulation of ossification 3% GO:0030324 lung development 3% GO:0030334 regulation of cell migration 3% GO:0030513 positive regulation of BMP signaling pathway 3% GO:0030514 negative regulation of BMP signaling pathway 3% GO:0031060 regulation of histone methylation 3% GO:0031103 axon regeneration 3% GO:0031109 microtubule polymerization or depolymerization 3% GO:0031115 negative regulation of microtubule polymerization 3% GO:0031338 regulation of vesicle fusion 3% GO:0031340 positive regulation of vesicle fusion 3% GO:0031570 DNA integrity checkpoint 3% GO:0032331 negative regulation of chondrocyte differentiation 3% GO:0032355 response to estradiol stimulus 3% GO:0032387 negative regulation of intracellular transport 3% GO:0032963 collagen metabolic process 3% GO:0032984 macromolecular complex disassembly 3% GO:0034470 ncRNA processing 3% GO:0034599 cellular response to oxidative stress 3% GO:0034614 cellular response to reactive oxygen species 3% GO:0034623 cellular macromolecular complex disassembly 3% GO:0034641 cellular nitrogen compound metabolic process 3% GO:0034644 cellular response to UV 3% GO:0034645 cellular macromolecule biosynthetic process 3% GO:0034660 ncRNA metabolic process 3% GO:0035107 appendage morphogenesis 3% GO:0035108 limb morphogenesis 3% GO:0035457 cellular response to interferon-alpha 3% GO:0035909 aorta morphogenesis 3% GO:0035988 chondrocyte proliferation 3% GO:0040001 establishment of mitotic spindle localization 3% GO:0040011 locomotion 3% GO:0040012 regulation of locomotion 3% GO:0040034 regulation of development, heterochronic 3% GO:0042060 wound healing 3% GO:0042273 ribosomal large subunit biogenesis 3% GO:0042330 taxis 3% GO:0042476 odontogenesis 3% GO:0042493 response to drug 3% GO:0042552 myelination 3% GO:0042692 muscle cell differentiation 3% GO:0042773 ATP synthesis coupled electron transport 3% GO:0042775 mitochondrial ATP synthesis coupled electron transport 3% GO:0043161 proteasomal ubiquitin-dependent protein catabolic process 3% GO:0043241 protein complex disassembly 3% GO:0043407 negative regulation of MAP kinase activity 3% GO:0044236 multicellular organismal metabolic process 3% GO:0045047 protein targeting to ER 3% GO:0045087 innate immune response 3% GO:0045333 cellular respiration 3% GO:0045597 positive regulation of cell differentiation 3% GO:0045667 regulation of osteoblast differentiation 3% GO:0045746 negative regulation of Notch signaling pathway 3% GO:0045765 regulation of angiogenesis 3% GO:0045766 positive regulation of angiogenesis 3% GO:0045768 positive regulation of anti-apoptosis 3% GO:0045837 negative regulation of membrane potential 3% GO:0045840 positive regulation of mitosis 3% GO:0046622 positive regulation of organ growth 3% GO:0048008 platelet-derived growth factor receptor signaling pathway 3% GO:0048145 regulation of fibroblast proliferation 3% GO:0048505 regulation of timing of cell differentiation 3% GO:0048545 response to steroid hormone stimulus 3% GO:0048562 embryonic organ morphogenesis 3% GO:0048568 embryonic organ development 3% GO:0048598 embryonic morphogenesis 3% GO:0048641 regulation of skeletal muscle tissue development 3% GO:0048678 response to axon injury 3% GO:0048704 embryonic skeletal system morphogenesis 3% GO:0048708 astrocyte differentiation 3% GO:0048714 positive regulation of oligodendrocyte differentiation 3% GO:0048715 negative regulation of oligodendrocyte differentiation 3% GO:0048742 regulation of skeletal muscle fiber development 3% GO:0048771 tissue remodeling 3% GO:0048863 stem cell differentiation 3% GO:0048864 stem cell development 3% GO:0048870 cell motility 3% GO:0050654 chondroitin sulfate proteoglycan metabolic process 3% GO:0050657 nucleic acid transport 3% GO:0050658 RNA transport 3% GO:0050678 regulation of epithelial cell proliferation 3% GO:0050679 positive regulation of epithelial cell proliferation 3% GO:0050768 negative regulation of neurogenesis 3% GO:0050773 regulation of dendrite development 3% GO:0050808 synapse organization 3% GO:0050920 regulation of chemotaxis 3% GO:0051028 mRNA transport 3% GO:0051095 regulation of helicase activity 3% GO:0051099 positive regulation of binding 3% GO:0051100 negative regulation of binding 3% GO:0051146 striated muscle cell differentiation 3% GO:0051153 regulation of striated muscle cell differentiation 3% GO:0051216 cartilage development 3% GO:0051225 spindle assembly 3% GO:0051236 establishment of RNA localization 3% GO:0051239 regulation of multicellular organismal process 3% GO:0051256 spindle midzone assembly involved in mitosis 3% GO:0051270 regulation of cellular component movement 3% GO:0051293 establishment of spindle localization 3% GO:0051305 chromosome movement towards spindle pole 3% GO:0051321 meiotic cell cycle 3% GO:0051327 M phase of meiotic cell cycle 3% GO:0051382 kinetochore assembly 3% GO:0051384 response to glucocorticoid stimulus 3% GO:0051443 positive regulation of ubiquitin-protein ligase activity 3% GO:0051569 regulation of histone H3-K4 methylation 3% GO:0051571 positive regulation of histone H3-K4 methylation 3% GO:0051592 response to calcium ion 3% GO:0051653 spindle localization 3% GO:0051656 establishment of organelle localization 3% GO:0051674 localization of cell 3% GO:0051707 response to other organism 3% GO:0051785 positive regulation of nuclear division 3% GO:0051823 regulation of synapse structural plasticity 3% GO:0051957 positive regulation of amino acid transport 3% GO:0055001 muscle cell development 3% GO:0060056 mammary gland involution 3% GO:0060071 Wnt receptor signaling pathway, planar cell polarity pathway 3% GO:0060174 limb bud formation 3% GO:0060219 camera-type eye photoreceptor cell differentiation 3% GO:0060249 anatomical structure homeostasis 3% GO:0060429 epithelium development 3% GO:0060537 muscle tissue development 3% GO:0060606 tube closure 3% GO:0060828 regulation of canonical Wnt receptor signaling pathway 3% GO:0060900 embryonic camera-type eye formation 3% GO:0060993 kidney morphogenesis 3% GO:0060998 regulation of dendritic spine development 3% GO:0061001 regulation of dendritic spine morphogenesis 3% GO:0061326 renal tubule development 3% GO:0061333 renal tubule morphogenesis 3% GO:0065003 macromolecular complex assembly 3% GO:0070206 protein trimerization 3% GO:0070482 response to oxygen levels 3% GO:0070972 protein localization in endoplasmic reticulum 3% GO:0071294 cellular response to zinc ion 3% GO:0071310 cellular response to organic substance 3% GO:0071345 cellular response to cytokine stimulus 3% GO:0071417 cellular response to organic nitrogen 3% GO:0071418 cellular response to amine stimulus 3% GO:0071453 cellular response to oxygen levels 3% GO:0071504 cellular response to heparin 3% GO:0071822 protein complex subunit organization 3% GO:0071843 cellular component biogenesis at cellular level 3% GO:0071845 cellular component disassembly at cellular level 3% GO:0071901 negative regulation of protein serine/threonine kinase activity 3% GO:0072009 nephron epithelium development 3% GO:0072028 nephron morphogenesis 3% GO:0072073 kidney epithelium development 3% GO:0072078 nephron tubule morphogenesis 3% GO:0072079 nephron tubule formation 3% GO:0072080 nephron tubule development 3% GO:0072088 nephron epithelium morphogenesis 3% GO:0072170 metanephric tubule development 3% GO:0072207 metanephric epithelium development 3% GO:0072210 metanephric nephron development 3% GO:0072224 metanephric glomerulus development 3% GO:0072234 metanephric nephron tubule development 3% GO:0072243 metanephric nephron epithelium development 3% GO:0072594 establishment of protein localization to organelle 3% GO:0072599 establishment of protein localization in endoplasmic reticulum 3% GO:0090092 regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 3% GO:0090101 negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 3% GO:0090175 regulation of establishment of planar polarity 3% GO:0090304 nucleic acid metabolic process 3% GO:0097066 response to thyroid hormone stimulus 3% GO:0097067 cellular response to thyroid hormone stimulus 3% GO:2000097 regulation of smooth muscle cell-matrix adhesion 3% GO:2000145 regulation of cell motility 3% GO:2000177 regulation of neural precursor cell proliferation 3% GO:2000179 positive regulation of neural precursor cell proliferation 3% GO:2000602 regulation of interphase of mitotic cell cycle

The % of individual tumors within a subgroup that are enriched for a specific GO term is shown, ordered by decreasing representation. Neurodevelopmental terms are highlighted with bolded text.

Discussion

The major finding is that AKT pathway genes classify GBM into at least five patient subgroups with unique clinical and molecular characteristics. The results were validated in an independent dataset of non-overlapping samples, suggesting AKT classes reflect underlying structure in the data and do not arise from chance or technical artifacts such as batch effects and patient sampling. Taken together these data add to previous results suggesting histopathologically diagnosed GBM is a collection of molecular subgroups with fundamental differences in biology and clinical behavior. This approach advances classification of GBM by splitting out groups not previously identified by other approaches and expands the understanding of molecular aberrations underlying subgroups.

The inventors interpret with caution the finding that SL patients treated with BCNU or CCNU have appreciably longer survival than SL patients receiving other treatments (median survival 5.8 vs. 1.05 years respectively). Inhomogeneity between the cohorts (including treatment protocols and institution providing tumor) could impact survival. However, age and IDH1 mutation status clearly do not contribute since patients in the longer surviving cohort were older and had less IDH1 mutations. These results suggest AKT classification is a predictive marker that identifies a subset of GBM patients with sensitivity to BCNU/CCNU. Interestingly, there is a subset of anaplastic oligodendroglial tumors characterized by 1p19q loss of heterozygosity (LOH) and IDH1 mutations that significantly benefits from procarbazine, CCNU, and vincristine (PCV) chemotherapy [35]. This anaplastic oligodendroglial subtype shares similarities to the AKT SL subgroup (19q loss and IDH1 mutant tumors).

Mutations in IDH1 are a common and early event in low grade glioma, they are present in secondary GBM [36], [37], [38] and may cause the G-CIMP phenotype [36], [37], [38], [39]. One third of SL tumors have IDH1 mutations and CIMP. This subgroup also has other molecular similarities to secondary tumors (enriched for genomic alterations in TP53 and PDGFRA), longer survival and a tendency for less endothelial proliferation and pallisading necrosis (FIGS. 12 and 13). These data suggest tumors in the SL subtype are grade IV secondary tumors or borderline grade III/IV secondary tumors progressing to GBM. If this is true then genomic alterations associated with the SL subtype might be used as markers of progression for grade II/III secondary tumors. These results also indicate there is a population of GBM without IDH1 mutations that share clinical characteristics and a similar pattern of AKT pathway gene expression with the IDH1 mutant tumors. This suggests other paths beside IDH1 mutation give rise to the IDH1 mutant/CIMP phenotype.

The inventors found distinct patterns of expression for PI3K/AKT/mTOR components in subgroups. The inventors' results suggest gene products that inhibit AKT and mTOR are important regulators of PI3K/AKT/mTOR/S6 axis output. In the inventors' model the loss of AKT and mTOR inhibitors (PHLPP, TSC and pAMPK) increases output of the AKT/mTOR/S6 axis in the MES subgroup. Conversely, increased expression of these inhibitors decreases output in the SL subgroup. In an apparent paradox, p-AKT expression is low in the MES subgroup. While not wishing to be bound by any theory, the inventors suggest AKT phosphorylation is held in check in the MES subgroup by (1) heightened activity of an mTOR/S6K/IRS1 negative feedback loop [40], [41], [42], [43] and (2) low TSC1 and 2 expression that decreases mTORC2 activation and AKT phosphorylation [42], [44]. The inventors' model suggests the MES subtype will be sensitive to joint inhibition of mTOR and PI3K, but inhibition of mTOR alone will increase p-AKT. Interestingly, NF1 loss drives mTOR/S6 hyper-activation via AKT [45], [46], [47] and the MES subtype is enriched for NF1 loss. These data suggest subgroups have variations in AKT pathway signaling that will affect sensitivity to pathway inhibitors.

How do these results compare with other approaches that use mRNA to classify GBM? AKT classification is complementary to previous classification methods but divides GBM into more subgroups. It gives patient subgroups with statistically significant differences in survival while Phillips [4] or TCGA [10] methods do not when using the same database. Interestingly, there was higher concordance between AKT classification and classification based on survival-associated mRNA used by Phillips et. al. [4] than most variable mRNA used by Verhaak et. al. [10]. Without wishing to be bound by any particular theory, the inventors believe classification schemes based on mRNA relevant to tumorigenicity, like survival-associated and AKT pathway genes, are more effective at partitioning tumors into clinically and molecularly relevant groups.

Survival differences found in the discovery dataset were diminished in the validation dataset. Inhomogeneity's between datasets that could confound comparisons including (1) age (median age=49 yrs. in discovery vs. 59 yrs. in validation dataset), (2) patient populations (three institutions contributed tumors to the discovery and eighteen to the validation dataset), (3) treatment (there were large variations in treatment regimens in the validation dataset).

One AKT subgroup was not found in the validation dataset (C1). While not wishing to be bound by any theory, morphological heterogeneity can result in inconsistent intra- and inter-observer diagnosis of grade and histological type (astrocytoma, oligodendroglioma and mixed oligoastrocytoma) [48], [49], [50]. Therefore C1 may be a histological variant diagnosed as GBM and included in the discovery, but not the validation dataset.

GO term analysis suggests different cells of origin/dominant biological processes for each subgroup (summarized in FIGS. 8A and B). The younger, longer surviving, SL patient subgroup with molecular similarities to secondary GBM had terms associated with both neuro- and glio-genesis suggesting a NSC cell of origin. Indeed, the longer survival of these patients is consistent with the quiescent nature of NSC. PROLIF tumors also contained neuro- and glio-genesis terms in addition to terms related to mitosis, spindle formation and cell cycle checkpoint. Literature suggests the balance between symmetric and asymmetric cell divisions regulates NSC [51] which is influenced by proteins with a role in spindle formation and mitotic progression [52]. Based on this and their aggressive nature, while not wishing to be bound by any theory, the inventors believe that PROLIF tumors are derived from NSC with enforced symmetric cell divisions that rapidly expand the population (FIG. 8B). The ability of AKT classification to group tumors by cell of origin would suggest a major role for the PI3K/AKT pathway in neurodevelopment. This is consistent with reports showing a role for pathway members in NSC maintenance [53], [54].

The inventors show that AKT-based classification can augment drug development on many levels. This work indicates evaluating new drugs using all GBM patients combined with different natural courses and/or response to therapy can confound clinical trials. It suggests incorporating AKT classification can improve clinical trial design, decreasing their cost and maximizing the number of therapeutics that can be evaluated. In addition, AKT based classification can enhance drug discovery since new pathways and drug targets will be easier to find in molecularly homogeneous samples. The inventors demonstrate that robust molecular classification of GBM can ultimately improve patient care by guiding therapeutic planning, sparing patients ineffective treatments, both standard and experimental, and focusing on strategies more likely to work.

Example 3: Mesenchymal Patients Benefit from Temozolomide

The AKT pathway can be a dominant determinant of response to diverse therapeutics including chemotherapy. The chemotherapy Temozolomide (TMZ; 6 cycles), is currently standard of care for newly diagnosed Glioblastoma. Here we show that AKT classification predicts response to TMZ in Glioblastoma.

We plotted Kaplan Meier survival curves for patients treated with more vs. less TMZ in each AKT subgroup (FIG. 17). Since most TCGA patients received some TMZ, it was not possible to plot survival curves for patients treated with and without the drug. Instead, we compared survival in 2 treatment arms, those receiving more (≥3) vs. less (<3) cycles.

We found that patients in the Secondary-Like subtype treated with more TMZ did worse than those receiving less. There was a tendency for patients who received more TMZ to not have received a nitrosourea. We showed evidence that CCNU/BCNU provides a 4.5 year survival advantage to Secondary-Like patients. Without wishing to be bound by any particular theory, this may underlie the worse survival of patients receiving more TMZ in the Secondary-Like subgroup. Also, we found that only Mesenchymal patients had a statistically significant difference in survival between treatment arms.

These results support that AKT classification is a biomarker identifying Glioblastoma patients responsive to TMZ.

Example 4

Generally

As disclosed herein, biomarkers that select patients for therapeutics would benefit clinical trial design and patient care. The Akt pathway is a therapeutic target in Glioblastoma Multiforme (GBM) and an important determinant of patient outcome. However, it is not known whether activity of this pathway varies among GBM tumors. To examine differences in AKT pathway among GBM, the inventors investigated mRNA expression of Akt pathway genes in published GBM expression datasets. It was found at least 6 distinct patterns of Akt pathway gene expression, and the patterns were prognostic. Pathway analysis suggests specific molecular targets within these Akt groups. Therefore Akt subgroups will help select patients for targeted therapies. Since Akt is an important determinant of response to conventional therapies, Akt subgroups will help select patients for conventional therapies.

Discussion

The inventors show there are at least 6 classes of GBM with different survival and patterns of Akt pathway gene expression. Survival differences suggest Akt class predicts either prognosis (tumor aggressiveness independent of therapy) or response to therapy. The Akt pathway is a partial determinant of sensitivity to both conventional and targeted therapies. Therefore the inventors believe that Akt class predicts response to conventional and targeted therapies. Other data supports this. EGFR and PDGFRα are established therapeutic targets in GBM. mRNA for these receptors is differentially expressed in subgroups. This supports Akt class can predict response to therapeutics targeting these receptors.

The inventors perform gene set enrichment analysis (GSE) using all profiled genes to find pathways activated in subgroups. The data showing EGFR and PDGFRα mRNA are subgroup specific and suggest different pathways are activated in subgroups. This supports mining subgroups for pathways will enhance target identification.

Conclusions

There are at least 6 classes of GBM with different patterns of Akt pathway gene expression. Furthermore, it demonstrates that Akt class can be used to match therapy to patient. Additionally, mining of Akt classes will enhance identification of subgroup-specific targets.

Methods and Materials

Analysis of the nucleic acid from an individual, whether amplified or not, may be performed using any of various techniques readily available and apparent to one of skill in the art. Useful techniques include, without limitation, polymerase chain reaction based analysis, sequence analysis and electrophoretic analysis. As used herein, the term “nucleic acid” means a polynucleotide such as a single or double-stranded DNA or RNA molecule including, for example, genomic DNA, cDNA and mRNA. The term nucleic acid encompasses nucleic acid molecules of both natural and synthetic origin as well as molecules of linear, circular or branched configuration representing either the sense or antisense strand, or both, of a native nucleic acid molecule.

Similarly, there are many techniques readily available in the field for detecting the presence or absence of polypeptides or other biomarkers, including protein microarrays. For example, some of the detection paradigms that can be employed to this end include optical methods, electrochemical methods (voltametry and amperometry techniques), atomic force microscopy, and radio frequency methods, e.g., multipolar resonance spectroscopy. Illustrative of optical methods, in addition to microscopy, both confocal and non-confocal, are detection of fluorescence, luminescence, chemiluminescence, absorbance, reflectance, transmittance, and birefringence or refractive index (e.g., surface plasmon resonance, ellipsometry, a resonant mirror method, a grating coupler waveguide method or interferometry).

Similarly, there are many techniques that may be employed to isolate and/or fractionate biomarkers. For example, a biomarker may be captured using biospecific capture reagents, such as antibodies, aptamers or antibodies that recognize the biomarker and modified forms of it. This method could also result in the capture of protein interactors that are bound to the proteins or that are otherwise recognized by antibodies and that, themselves, can be biomarkers. The biospecific capture reagents may also be bound to a solid phase. Then, the captured proteins can be detected by SELDI mass spectrometry or by eluting the proteins from the capture reagent and detecting the eluted proteins by traditional MALDI or by SELDI. One example of SELDI is called “affinity capture mass spectrometry,” or “Surface-Enhanced Affinity Capture” or “SEAC,” which involves the use of probes that have a material on the probe surface that captures analytes through a non-covalent affinity interaction (adsorption) between the material and the analyte. Some examples of mass spectrometers are time-of-flight, magnetic sector, quadrupole filter, ion trap, ion cyclotron resonance, electrostatic sector analyzer and hybrids of these.

Alternatively, for example, the presence of biomarkers such as polypeptides maybe detected using traditional immunoassay techniques. Immunoassay requires biospecific capture reagents, such as antibodies, to capture the analytes. The assay may also be designed to specifically distinguish protein and modified forms of protein, which can be done by employing a sandwich assay in which one antibody captures more than one form and second, distinctly labeled antibodies, specifically bind, and provide distinct detection of, the various forms. Antibodies can be produced by immunizing animals with the biomolecules. Traditional immunoassays may also include sandwich immunoassays including ELISA or fluorescence-based immunoassays, as well as other enzyme immunoassays.

Prior to detection, biomarkers may also be fractionated to isolate them from other components in a solution or of blood that may interfere with detection. Fractionation may include platelet isolation from other blood components, sub-cellular fractionation of platelet components and/or fractionation of the desired biomarkers from other biomolecules found in platelets using techniques such as chromatography, affinity purification, 1D and 2D mapping, and other methodologies for purification known to those of skill in the art. In one embodiment, a sample is analyzed by means of a biochip. Biochips generally comprise solid substrates and have a generally planar surface, to which a capture reagent (also called an adsorbent or affinity reagent) is attached. Frequently, the surface of a biochip comprises a plurality of addressable locations, each of which has the capture reagent bound there.

The PI3K/Akt Pathway is an Important Therapeutic Target in High Grade Glioma (HGG) and Many Other Cancers.

Akt is an oncogenic serine/threonine kinase that is a key effector in the PI3K/Akt pathway. This large and complex pathway regulates many functions important in cancer including migration, angiogenesis, proliferation, epithelial to mesenchyme transition (EMT) stem cell self-renewal and resistance to cytotoxic therapy. It does this by phosphorylating and regulating the activity of a large number of downstream effectors. There are currently>100 suspected Akt substrates and more are being discovered. A simplified schematic representation of this pathway is shown in FIG. 23 herein.

Akt is hyper-activated in the majority of high grade glioma (HGG) tumors and many other human cancers. Many inhibitors of this pathway are under development or are in clinical trial for treatment of cancer patients. It is not known if the pathway is used similarly among patients with a specific cancer. If different “branches” of the pathway are activated in different patients, this might determine how patients respond to targeted therapies. Since Akt is an important determinant of how cancer cells respond to chemotherapy and radiation, this applies to other anti-neoplastic and conventional therapies also.

Tumor Subtypes are Identified Based on Expression of PI3K/Akt Pathway Genes.

To investigate if the pathway is used differently among HGG patients, the inventors used expression of Akt pathway genes and clustering methods. The inventors generated a hand curated list of Akt pathway genes using PubMed literature searches and protein databases. The following categories were included: 1) upstream regulators and activators of Akt, 2) proteins that physically interact with Akt, 3) downstream effectors phosphorylated by Akt and 4) proteins in complexes known to interact with, regulate or be regulated by Akt (for example all proteins in mTORC1 and mTORC2).

The inventors generated a correlation between clustered samples plot (FIGS. 18A-18C) using the list of Akt pathway genes in a published expression profiling dataset containing 185 HGG and 14 non-neoplastic “autopsy” samples (FIG. 18A). This analysis gives information on the similarity of total Akt pathway gene expression between tumors. In FIG. 18A, tumors are plotted on both axis. If PI3K/Akt pathway genes of 2 tumors are positively correlated then the intersection of the 2 tumors is shown in red; intersection of tumors with negatively correlated Akt pathway gene expression are green; and intersections of tumors with little Akt pathway correlation are black.

This data shows that there are 6 patient subgroups that have similar expression of Akt pathway genes (non-clustering/cluster 0, and clusters 1-5, FIG. 18A) and a group of patients (lower left, FIG. 18A) that have gene expression profiles with low similarity to any cluster. Subgroups are associated with different survival curves (FIG. 18B). Difference between survival for patients in clusters 4 and 5 approached statistical significance (p=0.06 log rank test; FIG. 18C). This data shows tumor subgroups exist that regulate Akt pathway genes differently, and these subgroups use different “branches” of the Akt pathway. It follows that patient subgroups will respond to pathway inhibitors differently. They may also respond differently to chemotherapy and radiation.

Each subgroup may be analyzed for functional categories of genes. This may be accomplished by finding genes that are expressed differently between subgroups. The inventors used an unsupervised clustering method that classifies similar objects into groups. In this case tumors with similar expression of Akt pathway genes are clustered (FIGS. 19A-19D). Tumors are listed at the top and genes at the sides. If the expression of a gene is high in a tumor the intersection between gene and tumor is red; if it is low then green. These analyses should demonstrate which Akt pathway genes are important in each subgroup and therefore which inhibitors should work in specific subgroups. For example, a preliminary analysis shows that PDGFRα is overexpressed in subgroup 4 and EGFR is overexpressed in subgroup 3 (FIGS. 19A-19D). The inventors believe that patients in subgroup 4 will respond to PDGFRα inhibitors and patients in subgroup 3 will respond to EGFR inhibitors. Additionally, as readily apparent to one of skill in the art, any number of other analysis maybe used to find which Akt pathway genes are important in each subgroup. These analyses can also be used to find other genes, not necessarily directly associated with the Akt pathway, that are important to the Akt subgroup.

Summary

The inventors demonstrate there are 6 major subgroups of HGG that regulate Akt pathway genes differently. The inventors believe that these subgroups use different “branches” of the Akt pathway and will respond differently to conventional and targeted therapies. Therefore this analysis may be used to match therapy to patient. A potential benefit of this approach over current methods that analyze a single molecule or gene is that this analysis can allow a more comprehensive categorization of patients and selection between multiple therapy options.

Significance

The inventors believe that the described analysis can be used to match therapy to patient. Subgroups may define patients that will respond to specific therapies targeting growth factors or the PI3K/Akt pathway. They can also define patients that will respond to conventional therapies. Since the PI3K/Akt pathway is important in many other cancers these results can apply to other cancers. The same type of analysis performed on other cancer-associated pathways (Ras, Notch etc. . . . ) may also yield subgroups defining patients that will respond to targeted therapies against those pathways.

AKT Pathway Gene Expression Divides Human-Rodent GBM Xenografts into Classes.

The inventors used rodent models of human Akt class to test response to human therapies find if Akt class predicts response to therapy. FIG. 24A is an Akt pathway correlation map of gene expression data from replicates of 15 rodent glioma xenografts. The analysis indicates 4 Akt xenograft classes. It is evident that xenograft models are readily classified by Akt gene expression. Distribution of biological replicates indicated by colors next to the axes demonstrates excellent Akt class stability. Similarities between Akt pathway maps demonstrate xenografts mimic gene expression of parental tumors, consistent with published reports of xenograft models of other tumors. The inventors investigate relationships between human and rodent Akt classes by mapping Akt pathway gene expression from xenografts onto human tumors. It is found 15% of genes have different expression in xenografts compared to the human tumors. When these genes are removed 6 of 7 xenografts cluster with parental human tumors. These data demonstrate human-rodent xenografts model human Akt class.

Response to Therapy Depends on Akt Class in Human-Rodent Xenograft Models.

In FIG. 24B, the inventors analyzed whether xenograft drug sensitivity is associated with Akt class. Xenograft group 2 is more sensitive to temozolomide (TMZ) and temozolomide plus radiation (TMZ+RT) than group 4 (p<0.05). The data demonstrates TMZ sensitivity is associated with Akt class and that Akt class predicts therapeutic response.

TABLE 4 Possible List of Genes to Distinguish Subgroups Genetic loci and corresponding ID number SORBS 8470 sorbin and SH3 domain containing protein PPP2R2C 5522 protein phosphatase 2 regulatory subunit B gamma TP53 7157 tumor protein p53 PIK3C3 5289 phosphatidylinositol 3-kinase catalytic subunit type 3 FGFR3 2261 fibroblast growth factor receptor 3 PPP2R5B 5526 protein phosphatase 3 regulator subunit B beta Akt1 207 v-akt murine thymoma viral oncogene homolog 1 Akt1S1 84335 akt 1 substrate 1 HIF1A 3091 hypoxia inducible factor 1 alpha EIF4EBP1 1978 eukaryotic translation initiation factor 4E binding protein 1 EGFR 1956 epidermal growth factor receptor PDGFC 56034 platelet derived growth factor C PDGFA 5154 platelet derived growth factor alpha PHLPP 23239 PH domain and leucine rich repeat protein phosphatase PDGFRA 5156 alpha type platelet derived growth factor receptor RICTOR 253260 RPTOR independent companion of MTOR, complex 2 AKT1P 64400 AKT interacting protein TWIST 7291 twist family bHLH transcription factor CCND1 595 cyclin D1 MDM2 4193 mouse double minute 2 GAB2 9846 GRB2-associated-binding protein 2 HSP90B1 7184 heat shock protein 90 kDa beta member 1

TABLE 5 Genes that when used in clustering methods, may divide tumors into subgroups Entrez Gene ID No. Gene Name Official Symbol 1026 CDKN1A 1027 CDKN1B 1111 CHEK1 116986 AGAP2 1950 EGF 1956 EGFR 1978 EIF4EBP1 2034 EPAS1 207 AKT1 2260 FGFR1 2261 FGFR3 2263 FGFR2 23035 PHLPPL 2308 FOXO1 2309 FOXO3 23239 PHLPP 2475 FRAP1 2549 GAB1 2887 GRB10 2932 GSK3B 3091 HIF1A 3164 NR4A1 3265 HRAS 3316 HSPB2 3320 HSP90AA1 3479 IGF1 3481 IGF2 3611 ILK 3635 INPP5D 3667 IRS1 3791 KDR 3845 KRAS 4193 MDM2 4217 MAP3K5 4303 FOXO4 4515 MTCP1 4893 NRAS 4904 YBX1 5036 PA2G4 5154 PDGFA 5156 PDGFRA 5159 PDGFRB 5287 PIK3C2B 5289 PIK3C3 5290 PIK3CA 5293 PIK3CD 5295 PIK3R1 5515 PPP2CA 5518 PPP2R1A 5520 PPP2R2A 5521 PPP2R2B 5524 PPP2R4 5525 PPP2R5A 5526 PPP2R5B 5527 PPP2R5C 5529 PPP2R5E 5586 PKN2 5728 PTEN 572 BAD 5747 PTK2 57761 TRIB3 5829 PXN 5894 RAF1 595 CCND1 64223 GBL 65125 WNK1 6850 SYK 7157 TP53 7184 HSP90B1 7248 TSC1 7249 TSC2 7291 TWIST1 842 CASP9 8660 IRS2 8915 BCL10 9846 GAB2 9882 TBC1D4 117145 THEM4 253260 RICTOR 53834 FGFRL1 5522 PPP2R2C 57521 KIAA1303 84280 BTBD10 84335 AKT1S1 10000 AKT3 26060 APPL1 3326 HSP90AB1 56034 PDGFC 6198 RPS6KB1 64400 AKTIP 79109 MAPKAP1 80146 UXS1 80310 PDGFD 8470 SORBS2 208 AKT2

TABLE 6 The status of increased expression, decreased expression, or expression not changed significantly (minimal expression difference) of AKT pathway genes as shown in FIG. 10 TCGA GBM195 MES CLAS PROLIF SL PN MES CLAS PROLIF SL PN SYK INC DEC DEC NC DEC INC DEC DEC INC DEC SYK CFD INC DEC DEC DEC NC INC DEC DEC DEC DEC CFD INPP5D INC NC DEC NC NC INC NC DEC INC DEC INPP5D PDGFRB INC INC DEC DEC DEC INC INC DEC DEC DEC PDGFRB CDKN1A INC INC DEC DEC DEC INC INC DEC DEC DEC CDKN1A KDR INC INC DEC INC NC INC INC DEC DEC NC KDR EPAS1 INC INC DEC INC NC INC INC DEC DEC NC EPAS1 IRS2 NC INC DEC INC INC INC INC DEC DEC DEC IRS2 PDGFD INC INC DEC INC DEC INC INC DEC DEC DEC PDGFD PDGFA DEC INC DEC INC NC INC INC DEC DEC DEC PDGFA GRB10 INC INC DEC INC DEC INC INC INC DEC DEC GRB10 HSP90B1 INC NC INC INC DEC INC INC INC DEC DEC HSP90B1 PDK1 NC NC INC INC DEC NC INC INC DEC DEC PDK1 CHEK1 NC DEC INC INC DEC DEC NC INC DEC DEC CHEK1 EZH2 DEC NC INC INC DEC DEC DEC INC DEC DEC EZH2 EIF3E NC NC INC INC DEC DEC NC INC INC DEC EIF3E SRSF1 DEC NC INC INC DEC DEC INC INC NC DEC SRSF1 NRAS NC NC INC DEC DEC DEC INC INC DEC DEC NRAS SSB DEC NC INC NC DEC DEC NC NC DEC DEC SSB IRS1 INC DEC NC INC NC DEC DEC DEC DEC DEC IRS1 WNK1 NC DEC NC INC INC DEC DEC DEC DEC DEC WNK1 PKN2 DEC NC INC INC DEC DEC NC DEC DEC DEC PKN2 BCL10 INC NC INC NC DEC DEC DEC NC DEC DEC BCL10 TWIST1 INC INC DEC DEC DEC INC NC NC DEC DEC TWIST1 PKD2 INC INC DEC NC NC INC INC DEC DEC DEC PKD2 PALLD INC INC DEC DEC NC INC INC DEC DEC DEC PALLD HIF1A INC NC DEC INC DEC INC INC DEC DEC DEC HIF1A PDGFC INC INC DEC DEC DEC NC INC DEC DEC DEC PDGFC VIM INC INC DEC DEC DEC INC INC INC NC DEC VIM TRIB3 INC INC INC DEC DEC INC INC INC INC DEC TRIB3 EIF4EBP1 NC NC INC DEC DEC INC INC INC NC DEC EIF4EBP1 ACLY DEC INC INC INC DEC DEC INC INC NC DEC ACLY TP53 NC INC INC NC DEC NC INC INC INC DEC TP53 EIF3B NC NC INC NC DEC INC INC INC INC DEC EIF3B RAF1 DEC NC INC INC DEC NC INC INC INC DEC RAF1 CCND1 NC DEC INC INC DEC NC DEC INC INC DEC CCND1 EIF3H NC DEC INC INC DEC DEC DEC INC INC DEC EIF3H FYN DEC NC DEC INC NC DEC INC INC INC DEC FYN PHLPP1 DEC INC DEC INC INC DEC NC NC INC INC PHLPP1 GAB1 DEC INC DEC INC NC DEC INC NC INC NC GAB1 EGFR DEC INC DEC NC NC DEC INC DEC INC DEC EGFR EIF3G DEC INC NC NC DEC INC INC INC INC DEC EIF3G AKT1 NC INC NC NC DEC INC INC INC INC NC AKT1 CDC37 NC NC INC DEC DEC INC INC INC INC NC CDC37 TSC2 DEC NC INC INC NC NC INC INC INC INC TSC2 PPP2R1A DEC NC INC NC NC NC INC INC INC INC PPP2R1A HSP90AB1 NC DEC INC INC NC DEC INC INC INC INC HSP90AB1 MAPK8IP1 DEC NC NC INC INC DEC INC DEC INC INC MAPK8IP1 GAB2 NC NC DEC INC INC DEC DEC DEC INC INC GAB2 PIK3C2B DEC DEC NC INC INC DEC DEC DEC INC INC PIK3C2B TSC1 DEC NC DEC INC INC DEC DEC DEC INC INC TSC1 GSK3B DEC DEC INC INC INC DEC DEC INC NC INC GSK3B SORBS2 DEC DEC NC DEC INC NC DEC DEC DEC INC SORBS2 FGFR2 DEC DEC NC NC INC DEC DEC DEC DEC INC FGFR2 FGFR3 DEC INC DEC DEC INC DEC INC DEC DEC INC FGFR3 PPP2R2B DEC INC DEC NC INC DEC INC DEC NC INC PPP2R2B PIK3R1 DEC NC DEC INC INC DEC DEC DEC INC INC PIK3R1 MAP3K5 INC NC DEC INC INC NC NC DEC INC INC MAP3K5 ATXN1 NC NC DEC INC INC DEC NC DEC NC INC ATXN1 PPARGC1A DEC INC DEC DEC INC DEC NC DEC DEC INC PPARGC1A KRAS DEC NC INC INC INC DEC DEC NC DEC INC KRAS CDKN1B DEC NC INC INC NC DEC DEC INC INC DEC CDKN1B PIK3CA NC DEC INC INC DEC DEC DEC DEC INC DEC PIK3CA FOXO3 DEC DEC DEC INC INC DEC DEC DEC INC DEC FOXO3 MES CLAS PROLIF SL PN MES CLAS PROLIF SL PN NOTE: INC means increased expression; DEC means decreased expression; and NC means expression not changed significantly or minimal expression difference.

In various embodiments, a subgroup or subtype's expression pattern of AKT pathway components may be determined according to the validation dataset (TCGA) and the discovery dataset (GBM195) as shown in FIG. 10 and Table 6. In some embodiments, a subgroup or subtype's expression pattern of AKT pathway components may be determined according to the validation dataset (TCGA) as shown in FIG. 10 and Table 6. In other embodiments, a subgroup or subtype's expression pattern of AKT pathway components may be determined according to the discovery dataset (GBM195) as shown in FIG. 10 and Table 6.

As readily apparent to one of skill in the art, any number of genetic loci and/or biomarkers could be used to subgroup tumors and conditions, and the invention is not in any way limited to those genes listed in Table 2, Table 4, Table 5, or Table 6 herein. For example, other genes related, both directly and indirectly to the Akt pathway, could be clustered and thus used for subgrouping a condition, disease and/or tumor. Or, for example, other methods of identifying Akt subgroups include the use of biomarkers that include nucleic acid(s), protein(s), modified protein(s), mutated or modified nucleic acid(s), epigenetic changes or a change(s) in DNA copy number associated with Akt subgroups. Similarly, this analysis may be generalized to any cancer that has Akt pathway activation, and the invention is in no way limited to GBM.

REFERENCES

-   1. Ohgaki H, Kleihues P (2007) Genetic pathways to primary and     secondary glioblastoma. The American journal of pathology 170:     1445-1453. -   2. DeAngelis L M, Mellinghoff I K (2011) Virchow 2011 or how to     ID(H) human glioblastoma. Journal of clinical oncology: official     journal of the American Society of Clinical Oncology 29: 4473-4474. -   3. Nigro J M, Misra A, Zhang L, Smirnov I, Colman H, et al. (2005)     Integrated array-comparative genomic hybridization and expression     array profiles identify clinically relevant molecular subtypes of     glioblastoma. Cancer Res 65: 1678-1686. -   4. Phillips H S, Kharbanda S, Chen R, Forrest W F, Soriano R H, et     al. (2006) Molecular subclasses of high-grade glioma predict     prognosis, delineate a pattern of disease progression, and resemble     stages in neurogenesis. Cancer cell 9: 157-173. -   5. Atlas T C G (2008) Comprehensive genomic characterization defines     human glioblastoma genes and core pathways. Nature 455: 1061-1068. -   6. Bredel M, Scholtens D M, Harsh G R, Bredel C, Chandler J P, et     al. (2009) A network model of a cooperative genetic landscape in     brain tumors. Jama 302: 261-275. -   7. Mischel P S, Shai R, Shi T, Horvath S, Lu K V, et al. (2003)     Identification of molecular subtypes of glioblastoma by gene     expression profiling. Oncogene 22: 2361-2373. -   8. Noushmehr H, Weisenberger D J, Diefes K, Phillips H S, Pujara K,     et al. (2010) Identification of a CpG island methylator phenotype     that defines a distinct subgroup of glioma. Cancer cell 17: 510-522. -   9. Shen R, Mo Q, Schultz N, Seshan V E, Olshen A B, et al. (2012)     Integrative subtype discovery in glioblastoma using iCluster. PLoS     ONE 7: e35236. -   10. Verhaak R G, Hoadley K A, Purdom E, Wang V, Qi Y, et al. (2010)     Integrated genomic analysis identifies clinically relevant subtypes     of glioblastoma characterized by abnormalities in PDGFRA, IDH1,     EGFR, and NF1. Cancer Cell 17: 98-110. -   11. Brennan C, Momota H, Hambardzumyan D, Ozawa T, Tandon A, et     al. (2009) Glioblastoma subclasses can be defined by activity among     signal transduction pathways and associated genomic alterations.     PLoS ONE 4: e7752. -   12. Engelman J A (2009) Targeting PI3K signalling in cancer:     opportunities, challenges and limitations. Nature reviews Cancer 9:     550-562. -   13. Wen P Y, Lee E Q, Reardon D A, Ligon K L, Alfred Yung W K (2012)     Current clinical development of PI3K pathway inhibitors in     glioblastoma. Neuro-oncology 14: 819-829. -   14. Huang T T, Sarkaria S M, Cloughesy T F, Mischel P S (2009)     Targeted therapy for malignant glioma patients: lessons learned and     the road ahead. Neurotherapeutics: the journal of the American     Society for Experimental NeuroTherapeutics 6: 500-512. -   15. Stambolic V, MacPherson D, Sas D, Lin Y, Snow B, et al. (2001)     Regulation of PTEN transcription by p53. Molecular cell 8: 317-325. -   16. Singh B, Reddy P G, Goberdhan A, Walsh C, Dao S, et al. (2002)     p53 regulates cell survival by inhibiting PIK3CA in squamous cell     carcinomas. Genes & development 16: 984-993. -   17. Moelling K, Schad K, Bosse M, Zimmermann S, Schweneker M (2002)     Regulation of Raf-Akt Cross-talk. The Journal of biological     chemistry 277: 31099-31106. -   18. Wan X, Harkavy B, Shen N, Grohar P, Helman L J (2007) Rapamycin     induces feedback activation of Akt signaling through an     IGF-1R-dependent mechanism. Oncogene 26: 1932-1940. -   19. Han E K, Leverson J D, McGonigal T, Shah O J, Woods K W, et     al. (2007) Akt inhibitor A-443654 induces rapid Akt Ser-473     phosphorylation independent of mTORC1 inhibition. Oncogene 26:     5655-5661. -   20. Manning B D, Cantley L C (2007) AKT/PKB signaling: navigating     downstream. Cell 129: 1261-1274. -   21. Freije W A, Castro-Vargas F E, Fang Z, Horvath S, Cloughesy T,     et al. (2004) Gene expression profiling of gliomas strongly predicts     survival. Cancer research 64: 6503-6510. -   22. Yuan T L, Cantley L C (2008) PI3K pathway alterations in cancer:     variations on a theme. Oncogene 27: 5497-5510. -   23. Alfarano C, Andrade C E, Anthony K, Bahroos N, Bajec M, et     al. (2005) The Biomolecular Interaction Network Database and related     tools 2005 update. Nucleic Acids Research 33: D418-424. -   24. Rafael. A. Irizarry B M B, Collin F, Cope L M, Hobbs B, et     al. (2003) Summaries of Affymetrix GeneChip probe level data.     Nucleic Acids Research 31: e15. -   25. Monti S T P, Mesirov J, Golub T (2003) Consensus clustering: A     resampling-based method for class discovery and visualization of     gene expression microarray data. Machine Learning 52: 91-118. -   26. Rousseeuw P (1987) Silhouettes: A graphical aid to the     interpretation and validation of cluster analysis. Journal of     Computational and Applied Mathematics 20: 53-65. -   27. Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, et     al. (2007) Assessing the significance of chromosomal aberrations in     cancer: methodology and application to glioma. Proc Natl Acad Sci     USA 104: 20007-20012. -   28. Robinson J T, Thorvaldsdottir H, Winckler W, Guttman M, Lander E     S, et al. (2011) Integrative genomics viewer. Nature biotechnology     29: 24-26. -   29. Misra A, Pellarin M, Nigro J, Smirnov I, Moore D, et al. (2005)     Array comparative genomic hybridization identifies genetic subgroups     in grade 4 human astrocytoma. Clin Cancer Res 11: 2907-2918. -   30. Dunnett C W (1955) A multiple comparison procedure for comparing     several treatments with a control. Journal of the American     Statistical Association 50: 1096-1121. -   31. Kutner M H, Nachtsheim C, Neter J, Li W (2005) Applied Linear     Statistical Models. New York: McGraw-Hill. -   32. The Cancer Genome Atlas NCI, National Institutes of Health,     Bethesda, Md. Available: http://cancergenome.nih.gov/. -   33. West K A, Castillo S S, Dennis P A (2002) Activation of the     PI3K/Akt pathway and chemotherapeutic resistance. Drug Resist Updat     5: 234-248. -   34. Burton E C, Lamborn K R, Feuerstein B G, Prados M, Scott J, et     al. (2002) Genetic aberrations defined by comparative genomic     hybridization distinguish long-term from typical survivors of     glioblastoma. Cancer research 62: 6205-6210. -   35. French P E L, Gravendeel L, Rooi J, Eiler P, Idbaih A, et     al. (2012) Intrinsic molecular subtypes of glioma are prognostic and     predict benefit from adjuvant PCV chemotherapy in anaplastic     oligodendroglial brain tumors: A report from the EORTC study 26951Y     26951 Neuro Oncol. 14: OM-21. -   36. Balss J, Meyer J, Mueller W, Korshunov A, Hartmann C, et     al. (2008) Analysis of the IDH1 codon 132 mutation in brain tumors.     Acta neuropathologica 116: 597-602. -   37. Ichimura K, Pearson D M, Kocialkowski S, Backlund L M, Chan R,     et al. (2009) IDH1 mutations are present in the majority of common     adult gliomas but rare in primary glioblastomas. Neuro-oncology 11:     341-347. -   38. Parsons D W, Jones S, Zhang X, Lin J C, Leary R J, et al. (2008)     An integrated genomic analysis of human glioblastoma multiforme.     Science 321: 1807-1812. -   39. Turcan S, Rohle D, Goenka A, Walsh L A, Fang F, et al. (2012)     IDH1 mutation is sufficient to establish the glioma hypermethylator     phenotype. Nature 483: 479-483. -   40. Haruta T, Uno T, Kawahara J, Takano A, Egawa K, et al. (2000) A     rapamycin-sensitive pathway down-regulates insulin signaling via     phosphorylation and proteasomal degradation of insulin receptor     substrate-1. Molecular endocrinology 14: 783-794. -   41. Harrington L S, Findlay G M, Gray A, Tolkacheva T, Wigfield S,     et al. (2004) The TSC1-2 tumor suppressor controls insulin-PI3K     signaling via regulation of IRS proteins. The Journal of cell     biology 166: 213-223. -   42. Efeyan A, Sabatini D M (2010) mTOR and cancer: many loops in one     pathway. Current opinion in cell biology 22: 169-176. -   43. Hartley D, Cooper G M (2002) Role of mTOR in the degradation of     IRS-1: regulation of PP2A activity. Journal of cellular biochemistry     85: 304-314. -   44. Huang J, Dibble C C, Matsuzaki M, Manning B D (2008) The     TSC1-TSC2 complex is required for proper activation of mTOR     complex 2. Molecular and cellular biology 28: 4104-4115. -   45. Dasgupta B, Yi Y, Chen D Y, Weber J D, Gutmann D H (2005)     Proteomic analysis reveals hyperactivation of the mammalian target     of rapamycin pathway in neurofibromatosis 1-associated human and     mouse brain tumors. Cancer research 65: 2755-2760. -   46. Banerjee S, Crouse N R, Emnett R J, Gianino S M, Gutmann D     H (2011) Neurofibromatosis-1 regulates mTOR-mediated astrocyte     growth and glioma formation in a TSC/Rheb-independent manner.     Proceedings of the National Academy of Sciences of the United States     of America 108: 15996-16001. -   47. Johannessen C M, Reczek E E, James M F, Brems H, Legius E, et     al. (2005) The NF1 tumor suppressor critically regulates TSC2 and     mTOR. Proceedings of the National Academy of Sciences of the United     States of America 102: 8573-8578. -   48. Everitt B (2006) The Cambridge dictionary of statistics. New     York: Cambridge University Press. -   49. Coons S W, Johnson P C, Scheithauer B W, Yates A J, Pearl D     K (1997) Improving diagnostic accuracy and interob server     concordance in the classification and grading of primary gliomas.     Cancer 79: 1381-1393. -   50. Mittler M A, Walters B C, Stopa E G (1996) Observer reliability     in histological grading of astrocytoma stereotactic biopsies.     Journal of neurosurgery 85: 1091-1094. -   51. Gotz M, Huttner W B (2005) The cell biology of neurogenesis.     Nature reviews Molecular cell biology 6: 777-788. -   52. Sakai D, Dixon J, Dixon M J, Trainor P A (2012) Mammalian     neurogenesis requires Treacle-Plk1 for precise control of spindle     orientation, mitotic progression, and maintenance of neural     progenitor cells. PLoS genetics 8: e1002566. -   53. Groszer M, Erickson R, Scripture-Adams D D, Dougherty J D, Le     Belle J, et al. (2006) PTEN negatively regulates neural stem cell     self-renewal by modulating G0-G1 cell cycle entry. Proc Natl Acad     Sci USA 103: 111-116. -   54. Sinor A D, Lillien L (2004) Akt-1 expression level regulates CNS     precursors. J Neurosci 24: 8531-8541. -   55. Brennan C W, Verhaak R G, McKenna A, Campos B, Noushmehr H, et     al. (2013) The somatic genomic landscape of glioblastoma. Cell 155:     462-477. -   56. Network TCGAR (2008) Comprehensive genomic characterization     defines human glioblastoma genes and core pathways. Nature 455:     1061-1068.

The various methods and techniques described above provide a number of ways to carry out the application. Of course, it is to be understood that not necessarily all objectives or advantages described can be achieved in accordance with any particular embodiment described herein. Thus, for example, those skilled in the art will recognize that the methods can be performed in a manner that achieves or optimizes one advantage or group of advantages as taught herein without necessarily achieving other objectives or advantages as taught or suggested herein. A variety of alternatives are mentioned herein. It is to be understood that some preferred embodiments specifically include one, another, or several features, while others specifically exclude one, another, or several features, while still others mitigate a particular feature by inclusion of one, another, or several advantageous features.

Furthermore, the skilled artisan will recognize the applicability of various features from different embodiments. Similarly, the various elements, features and steps discussed above, as well as other known equivalents for each such element, feature or step, can be employed in various combinations by one of ordinary skill in this art to perform methods in accordance with the principles described herein. Among the various elements, features, and steps some will be specifically included and others specifically excluded in diverse embodiments.

Although the application has been disclosed in the context of certain embodiments and examples, it will be understood by those skilled in the art that the embodiments of the application extend beyond the specifically disclosed embodiments to other alternative embodiments and/or uses and modifications and equivalents thereof.

Preferred embodiments of this application are described herein, including the best mode known to the inventors for carrying out the application. Variations on those preferred embodiments will become apparent to those of ordinary skill in the art upon reading the foregoing description. It is contemplated that skilled artisans can employ such variations as appropriate, and the application can be practiced otherwise than specifically described herein. Accordingly, many embodiments of this application include all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the application unless otherwise indicated herein or otherwise clearly contradicted by context.

All patents, patent applications, publications of patent applications, and other material, such as articles, books, specifications, publications, documents, things, and/or the like, referenced herein are hereby incorporated herein by this reference in their entirety for all purposes, excepting any prosecution file history associated with same, any of same that is inconsistent with or in conflict with the present document, or any of same that may have a limiting affect as to the broadest scope of the claims now or later associated with the present document. By way of example, should there be any inconsistency or conflict between the description, definition, and/or the use of a term associated with any of the incorporated material and that associated with the present document, the description, definition, and/or the use of the term in the present document shall prevail.

It is to be understood that the embodiments of the application disclosed herein are illustrative of the principles of the embodiments of the application. Other modifications that can be employed can be within the scope of the application. Thus, by way of example, but not of limitation, alternative configurations of the embodiments of the application can be utilized in accordance with the teachings herein. Accordingly, embodiments of the present application are not limited to that precisely as shown and described.

Various embodiments of the invention are described above in the Detailed Description. While these descriptions directly describe the above embodiments, it is understood that those skilled in the art may conceive modifications and/or variations to the specific embodiments shown and described herein. Any such modifications or variations that fall within the purview of this description are intended to be included therein as well. Unless specifically noted, it is the intention of the inventors that the words and phrases in the specification and claims be given the ordinary and accustomed meanings to those of ordinary skill in the applicable art(s).

The foregoing description of various embodiments of the invention known to the applicant at this time of filing the application has been presented and is intended for the purposes of illustration and description. The present description is not intended to be exhaustive nor limit the invention to the precise form disclosed and many modifications and variations are possible in the light of the above teachings. The embodiments described serve to explain the principles of the invention and its practical application and to enable others skilled in the art to utilize the invention in various embodiments and with various modifications as are suited to the particular use contemplated. Therefore, it is intended that the invention not be limited to the particular embodiments disclosed for carrying out the invention.

While particular embodiments of the present invention have been shown and described, it will be obvious to those skilled in the art that, based upon the teachings herein, changes and modifications may be made without departing from this invention and its broader aspects and, therefore, the appended claims are to encompass within their scope all such changes and modifications as are within the true spirit and scope of this invention. 

1-29. (canceled)
 30. A method for treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of a cancer in a subject, comprising: assaying a sample obtained from the subject to detect increases and/or decreases in expression levels of AKT pathway components relative to reference samples or values, wherein the AKT pathway components is selected from the group consisting of ATP citrate lyase (ACLY), V-akt murine thymoma viral oncogene homolog 1 (AKT1), Ataxin 1 (ATXN1), B-cell CLL/lymphoma 10 (BCL10), Cyclin D1 (CCND1), Cell division cycle 37 (CDC37), Cyclin-dependent kinase inhibitor 1A (CDKN1A), Cyclin-dependent kinase inhibitor 1B (CDKN1B), Complement factor D (CFD), Checkpoint kinase 1 (CHEK1), Epidermal growth factor receptor (EGFR), Eukaryotic translation initiation factor 3 subunit B (EIF3B), Eukaryotic translation initiation factor 3 subunit E (EIF3E), Eukaryotic translation initiation factor 3 subunit G (EIF3G), Eukaryotic translation initiation factor 3 subunit F (EIF3H), Eukaryotic translation initiation factor 4E binding protein 1 (EIF4EBP1), Endothelial PAS domain protein 1 (EPAS1), Enhancer of zeste homolog 2 (EZH2), Fibroblast growth factor receptor 2 (FGFR2), Fibroblast growth factor receptor 3 (FGFR3), Forkhead box 03 (FOXO3), FYN oncogene related to SRC FGR YES (FYN), GRB2-associated binding protein 1 (GAB1), GRB2-associated binding protein 2 (GAB2), Growth factor receptor-bound protein 10 (GRB10), Glycogen synthase kinase 3 beta (GSK3B), Hypoxia inducible factor 1, alpha subunit (HIF1A), Heat shock protein 90 alpha (cytosolic) class B member 1 (HSP90AB1), Heat shock protein 90 beta (Grp94) member 1 (HSP90B1), Inositol polyphosphate-5-phosphatase (INPP5D), Insulin receptor substrate 1 (IRS1), Insulin receptor substrate 2 (IRS2), Kinase insert domain receptor (KDR), V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS), Mitogen-activated protein kinase kinase kinase 5 (MAP3K5), Mitogen-activated protein kinase 8 interacting protein 1 (MAPK8IP1), Neuroblastoma RAS viral (v-ras) oncogene homolog (NRAS), Palladin, cytoskeletal associated protein (PALLD), Platelet-derived growth factor alpha (PDGFA), platelet derived growth factor C (PDGFC), Platelet derived growth factor D (PDGFD), Platelet-derived growth factor receptor beta (PDGFRB), 3-phosphoinositide dependent protein kinase-1 (PDK1), PH domain and leucine rich repeat protein phosphatase 1 (PHLPP1), Phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta (PIK3C2B), Phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA), Phosphoinositide-3-kinase, regulatory subunit 1 (alpha) (PIK3R1), Polycystic kidney disease 2 (PKD2), Protein kinase N2 (PKN2), Peroxisome proliferator-activated receptor gamma, coactivator 1 alpha (PPARGC1A), Protein phosphatase 2 regulatory subunit A alpha (PPP2R1A), Protein phosphatase 2 regulatory subunit B beta (PPP2R2B), V-raf-1 murine leukemia viral oncogene homolog 1 (RAF1), Sorbin and SH3 domain containing 2 (SORBS2), Serine/arginine-rich splicing factor 1 (SRSF1), Sjogren syndrome antigen B (SSB), Spleen tyrosine kinase (SYK), Tumor protein p53 (TP53), Tribbles homolog 3 (TRIB3), Tuberous sclerosis 1 (TSC1), Tuberous sclerosis 2 (TSC2), Twist basic helix-loop-helix transcription factor 1 (TWIST1), Vimentin (VIM), WNK lysine deficient protein kinase 1 (WNK1), and combinations thereof; detecting an expression pattern of AKT pathway components in the sample based on the detected increases and/or decreases, wherein the expression pattern of AKT pathway components is C1 ‘s expression pattern, PN's expression pattern, MES's expression pattern, CLAS's expression pattern of AKT pathway components, SL's expression pattern, or PROLIF’ s expression pattern, and wherein C1's expression pattern comprise increased expression levels in one or more of ATXN1, BCL10, CDKN1B, CFD, CHEK1, EIF3E, EIF3H, EPAS1, EZH2, FOXO3, HIF1A, HSP90B1, IRS1, IRS2, KRAS, MAP3K5, NRAS, PALLD, PDGFA, PDGFC, PDGFD, PDK1, PIK3CA, PIK3R1, PKD2, PKN2, PPARGC1A, PPP2R2B, SRSF1, SSB, SYK, TWIST1, and WNK1; and/or insignificantly changed expression levels in one or more of CCND1, CDKN1A, KDR, TRIB3, and VIM; and/or decreased expression levels in one or more of ACLY, AKT1, CDC37, EGFR, EIF3B, EIF3G, EIF4EBP1, FGFR2, FGFR3, FYN, GAB1, GAB2, GRB10, GSK3B, HSP90AB1, INPP5D, MAPK8IP1, PDGFRB, PHLPP1, PIK3C2B, PPP2R1A, RAF1, SORBS2, TP53, TSC1, and TSC2; PN's expression pattern of AKT pathway components comprise increased expression levels in one or more of ATXN1, FGFR2, FGFR3, GAB2, GSK3B, HSP90AB1, IRS1, KRAS, MAP3K5, MAPK8IP1, PHLPP1, PIK3C2B, PIK3R1, PPARGC1A, PPP2R1A, PPP2R2B, SORBS2, TSC1, and TSC2; and/or insignificantly changed expression levels in one or more of CDKN1B, CFD, EPAS1, FOXO3, GAB1, KDR, and WNK1; and/or decreased expression levels in one or more of ACLY, AKT1, BCL10, CCND1, CDC37, CDKN1A, CHEK1, EGFR, EIF3B, EIF3E, EIF3G, EIF3H, EIF4EBP1, EZH2, FYN, GRB10, HIF1A, HSP90B1, INPP5D, IRS2, NRAS, PALLD, PDGFA, PDGFC, PDGFD, PDGFRB, PDK1, PIK3CA, PKD2, PKN2, RAF1, SRSF1, SSB, SYK, TP53, TRIB3, TWIST1, and VIM; MES's expression pattern of AKT pathway components comprise increased expression levels in one or more of AKT1, BCL10, CCND1, CDC37, CDKN1A, CFD, EIF3B, EPAS1, GRB10, HIF1A, HSP90B1, INPP5D, IRS1, IRS2, KDR, PALLD, PDGFA, PDGFC, PDGFD, PDGFRB, PDK1, PKD2, SYK, TRIB3, TWIST1, and VIM; and/or insignificantly changed expression levels in one or more of CHEK1, EIF3G, EIF4EBP1, MAP3K5, PKN2, SORBS2, TP53, and WNK1; and/or decreased expression levels in one or more of ACLY, ATXN1, CDKN1B, EGFR, EIF3E, EIF3H, EZH2, FGFR2, FGFR3, FOXO3, FYN, GAB1, GAB2, GSK3B, HSP90AB1, KRAS, MAPK8IP1, NRAS, PHLPP1, PIK3C2B, PIK3CA, PIK3R1, PPARGC1A, PPP2R1A, PPP2R2B, RAF1, SRSF1, SSB, TSC1, and TSC2; CLAS's expression pattern of AKT pathway components comprise increased expression levels in one or more of ACLY, AKT1, CDC37, CDKN1A, CHEK1, EGFR, EIF3B, EIF3E, EIF3G, EIF4EBP1, EPAS1, FGFR3, FYN, GAB1, GRB10, HIF1A, HSP90B1, IRS2, KDR, MAPK8IP1, NRAS, PALLD, PDGFA, PDGFC, PDGFD, PDGFRB, PDK1, PKD2, PKN2, PPARGC1A, PPP2R1A, PPP2R2B, RAF1, SRSF1, SSB, TP53, TRIB3, TWIST1, and VIM; and/or insignificantly changed expression levels in one or more of ATXN1, BCL10, EIF3H, EZH2, HSP90AB1, INPP5D, PIK3R1, and SYK; and/or decreased expression levels in one or more of CCND1, CDKN1B, CFD, FGFR2, FOXO3, GAB2, GSK3B, IRS1, KRAS, MAP3K5, PHLPP1, PIK3C2B, PIK3CA, SORBS2, TSC1, TSC2, and WNK1; SL's expression pattern of AKT pathway components comprise increased expression levels in one or more of ACLY, CCND1, CDKN1B, EGFR, EIF3B, EIF3E, EIF3G, EIF3H, FOXO3, FYN, GAB1, GAB2, INPP5D, IRS1, MAP3K5, MAPK8IP1, PDGFC, PHLPP1, PIK3C2B, PIK3CA, PIK3R1, RAF1, SYK, TP53, TRIB3, TSC1, and TSC2; and/or insignificantly changed expression levels in one or more of ATXN1, CDC37, GSK3B, HSP90AB1, PKN2, PPP2R2B, and SRSF1; and/or decreased expression levels in one or more of AKT1, BCL10, CDKN1A, CFD, CHEK1, EIF4EBP1, EPAS1, EZH2, FGFR2, FGFR3, GRB10, HIF1A, HSP90B1, IRS2, KDR, KRAS, NRAS, PALLD, PDGFA, PDGFD, PDGFRB, PDK1, PKD2, PPARGC1A, PPP2R1A, SORBS2, SSB, TWIST1, VIM, and WNK1; and PROLIF's expression pattern of AKT pathway components comprise increased expression levels in one or more of ACLY, AKT1, BCL10, CCND1, CDKN1B, CHEK1, EIF3B, EIF3E, EIF3G, EIF3H, EIF4EBP1, EZH2, FYN, GSK3B, HSP90AB1, HSP90B1, NRAS, PDK1, PIK3CA, PPP2R1A, RAF1, SRSF1, SSB, TP53, TRIB3, TSC2, and TWIST1; and/or insignificantly changed expression levels in one or more of CDC37, GAB1, GRB10, IRS1, KRAS, PHLPP1, PKN2, and VIM; and/or decreased expression levels in one or more of ATXN1, CDKN1A, CFD, EGFR, EPAS1, FGFR2, FGFR3, FOXO3, GAB2, HIF1A, INPP5D, IRS2, KDR, MAP3K5, MAPK8IP1, PALLD, PDGFA, PDGFC, PDGFD, PDGFRB, PIK3C2B, PIK3R1, PKD2, PPARGC1A, PPP2R2B, SORBS2, SYK, TSC1, and WNK1; and administering a therapeutically effective amount of a therapeutic to the subject, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of the cancer.
 31. The method of claim 30, wherein the cancer is a brain tumor, glioma, high grade glioma (HGG), glioblastoma, or glioblastoma multiforme (GBM).
 32. The method of claim 30, wherein the subgroup is subgroup SL, and wherein the therapeutic is BCNU or CCNU, a functional equivalent, analog, derivative or salt of BCNU or CCNU, or a combination thereof.
 33. The method of claim 32, further comprising preventing the subject from receiving TMZ, or a functional equivalent, analog, derivative or salt of TMZ.
 34. The method of claim 30, wherein the subgroup is subgroup MES, and wherein the therapeutic is TMZ, a functional equivalent, analog, derivative or salt of TMZ, or a combination thereof.
 35. The method of claim 30, further comprising detecting a marker for the ATK expression pattern.
 36. The method of claim 35, wherein the marker is one or more mutations in IDH1, IDH2 or both.
 37. The method of claim 35, wherein the marker is an increased expression level in VIM, CD44, CD45, Fibronectin, or Nucleostemin, or a combination thereof.
 38. The method of claim 35, wherein the marker is one or more mutations in EGFR and/or CDKN2A, or copy number alterations (CNAs), or combinations thereof.
 39. A method for treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of a cancer in a subject, comprising: administering a therapeutically effective amount of TMZ, a functional equivalent, analog, derivative or salt of TMZ to the subject, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of the cancer, wherein the subject has been detected as having a MES subgroup/subtype cancer or a marker for the MES subgroup/subtype, wherein the therapeutic is TMZ, a functional equivalent, analog, derivative or salt of TMZ, or a combination thereof. 